Quick-XAFS

Introduction

X-ray absorption techniques such as x-ray absorption near-edge spectroscopy (XANES) and extended x-

ray absorption fine structure (EXAFS) can be used to determine the local coordination environment and

oxidation state of nano-crystalline and amorphous materials.1 These techniques are important to the

study of catalytic processes wherein the catalytic materials undergo change of phase through red-ox

reactions and or deactivation. Conventional x-ray absorption techniques can take a “snap shot” of the

catalyst phase during a reactions progress via ex situ methods where care is taken to prevent oxidation

or preferentially, via in situ methods where a passivated (oxidized) catalyst is reduced. However, during

in situ studies all data between the oxidized and reduced catalyst phase is lost due to the poor time

resolution of conventional X-ray absorption data acquisition techniques. The time over which the scan

takes place is slow: the monochromator accelerates, decelerates, stops, data is collected over a one or

two second integration time, etc.

In order to speed up the rate at which x-ray absorption data can be acquired two divergent techniques

have been employed. The x-ray dispersive technique utilizes a polychromatic x-ray beam and a bent

monochromator that allows for spatial resolution of energy levels across a photodiode array. These

techniques were pioneered as early as 1986 by Dartyge and colleagues.2 This technique allows for fast

data collection but generates noisy data because higher harmonics can not be easily detuned from the

spectra. Another technique used at X18B of the National Synchrotron Light Source employs a double

crystal monochromator that is coupled to a micro-stepping motor and cam. In this technique data is

collected “on the fly” while the monochromator selectively permits x-rays of a specific energy to pass

through it by Bragg diffraction. This technique has was used by Murphy and colleagues to reduce the

data acquisition time to 50% of the conventional x-ray absorption scan.3 Using this technique the time

of data acquisition is sped up because the monochromator needs to decelerate, stop, and accelerate

only when it reaches its maximum and minimum bragg angles. The resulting energy of the diffracted x-

rays ultimately varies as a quasi-sinusoidal function of time.

Since the studies of Murphy and colleagues many advances in data acquisition techniques have been

made which allow for quicker data acquisition and subsequently better time resolution of x-ray

absorption spectra. These improvements ultimately allow for the reliable application of quick x-ray

absorption techniques to study the kinetics of catalyst phase transformations. Quick x-ray absorption

techniques pioneered at Brookhaven National Laboratory’s (BNL) National Synchrotron Light Source

(NSLS) are proving to be reliable in imaging the in situ phase transformation of nano-particulate

catalysts. These QXAFS data are being comparatively analyzed with fractional conversion and product

selectivity data acquired via SCC gas handling systems to develop new theories, prove reaction

mechanisms and ultimately design more efficient catalysts and chemical processes.

[1] Koningsberger, D. Prins, R. Chemical Analysis 1988 92

[2] Dartyge, E. Depautex, C. Dubuisson, J. Fontane, A. Jucha, A. Leboucher, P. Tourillon Nuc. Inst. and

Methods A 1986 246 452-460

[3] Murphy, L. Dobson, B. Neu, M. Ramsdale, C. Stange, R. Hasnain, S. J. Synchrotron Rad. 1995 2 64-69

X18B Technique

Beamline X18B of the SCC is capable of collecting and processing quick-XAFS data. The current data

acquisition method collects 60K points/minute using a Keithley current amplifier, a sixteen channel VME

analog-digital-converter (ADC), and custom programmed Linux based software. The bragg angle of a

Si(111) double crystal monochromator is controlled via an assembly containing a micro-stepping motor,

a rotating cam, and a small brass lever arm directly attached to the monochromator tangent arm [Figure

1]. This setup results in high resolution quick-XAFS energy data that varies as sinusoidal function of time

with a frequency that is inversely proportional to the time resolution of the quick-XAFS scan. This data is

then processed with Crop Chop series software to provide users with individual and time resolved EXAFS

or XANES scans that can be analyzed in Athena or Origin.

Figure 1. A close up of the cam and the small brass lever arm. The rotating cam moves the small lever

arm that is coupled to the monochromator tangent arm up and down around the pivot-point.

Crop N’ Chop 2.0

Crop N’ Chop 2.0 (CNC) will process Quick X-ray absorption fine data (QXAD) collected at Brookhaven

National Laboratory National Synchrotron Light Source beam lines X18B, and X19A. This program

enables the user to create time resolved EXAFS or XANES scans of in-situ chemical transformations by

outputting ASCII data files that can be plotted in programs such as Origin. Ultimately, data processed

with Crop Chop series programs will enable Synchrotron Catalysis Consortium users to elucidate the role

that nano-catalysts play in chemical reactions.

About this Manual

This manual will help you to become familiar with the Crop N’ Chop 2.0 environment and its method of

Quick X-ray absorption spectroscopy data processing. It completes this objective by providing exercises

that will guide you through the processing and calibration of QXAD using CNC, related software, and

other techniques. After you complete basic exercises using the CNC software detailed information about

the algorithms and principles on which CNC operate are presented. This will enable you to tailor your

data collection techniques to ensure that the data you process with CNC is precise and presentable.

Section 1: An Introduction to Crop and Chop via Examples

1.1 Program Activation for CNC Copies Acquired via Email or the SCC website

1) Unzip the contents of the Crop and Chop 2.0.zip file. Programs such as WinZip or WinRAR can be used

for this purpose. Trial versions of these programs can be downloaded free of charge from

www.winzip.com and www.win-rar.com.

2) Rename the Crop and Chop executable file with extension .ex to .exe. Make sure that the file Crop

and Chop 2.0.ex file is not confused with the example files that are named CC20.ex1, CC20.ex2, etc.

1.2 Example: Basic File Processing

1) CC20.ex1 is located in the directory which contains the Crop and Chop 2.0 executable. CC20.ex1 is an

ASCII file containing data collected at X18B from a Cu foil which should be viewed with WordPad.

a) There are seven rows, one of which is labeled time. The time contained in this row is the start time of

the Quick X-ray absorption scan in Linux time.

b) Note that in the file there are 5 columns below the first seven rows. These columns correspond to

time, Io, It, PIPS and the Heidenhain encoder respectively.

2) Run the Crop N’ Chop executable.

3) “Enter the edge energy in eV of the element under investigation.” The CC20.ex1 is a Cu foil QXANES

scan which was collected in fluorescence mode. The edge energy of Cu foil is ‘8979’ eV. Enter this value

and press enter on the keyboard.

a) Crop and Chop 2.0 will implement a check to ensure that you have entered the correct value of Eo. If

the proper value of Eo was entered type ‘yes’ and press enter on the keyboard.

b) Or else enter ‘no’ and press enter to repeat step 3.

4) “Enter the Heidenhain encoder value at Eo.” The Heindenhain encoder value is the digital signal that

corresponds to the Bragg angle of the monochromator. A linear relationship with a fixed slope is used to

model the relationship between the digital signal and the Bragg angle of the monochromator. Therefore,

one point in the spectra must be specified in order to model the energy of the X-rays that are permitted

to pass through the monochromator at any time in the scan. Eo is chosen because it can be identified

easily with the condition that it occurs where dMu/dE=max. The process of determining this value will

be explained in Section 4. For this series of spectra it was determined that the Heidenhain encoder value

at Eo was ‘-4040478839701’. Enter this value and press enter on the keyboard.

a) Crop and Chop will implement a check to ensure the correct value of Heidenhain encoder value was

entered. If the proper value was entered type ‘yes’ and press enter on the keyboard.

b) Or else enter ‘no’ and press enter to repeat step 4.

5) Next CNC will request the range of data that you would like to have processed in the scan. This data

contained in this QXANES scan has an energy range which is roughly from 8920 eV to 9100 eV.

a) “Enter how far below the edge in eV data should be processed.” Enter ‘50’ and press enter.

b) “Enter how far above the edge in eV data should be processed.” Enter ‘100’ and press enter.

c) CNC will implement a check to ensure the correct energy range has been entered. The energy range

should be from 8929 to 9079. If the proper energy range was entered type ‘yes’ and press enter on the

keyboard. Or else enter ‘no’ and press enter to repeat step 5.

d) Note that we did not extend our data processing range to the limits of the range of data that was

collected. The Crop and Chop algorithm will not split the data files if we give it the maximum and

minimums of our energy range. When you are processing your data play with the limits to find the

largest range of data that will allow CNC to chop your QXAD files into the proper number of spectra.

6) “Would you like to process multiple files which are arranged in chronological order?” Enter ‘no’. This

function accesses CNC’s Agglomerate function which can be used to process QXAFS data files that were

collected successively with SCC QXAD acquisition techniques.

7) “What would you like to name the directory were your files will be stored?” Enter ‘Cuf’ and press

enter.

8) “Enter the number of files that you would like to have processed.” Enter ‘1’ and press enter. In this

example only CC20.ex1 will be processed. CNC has the capability of processing many files during one

execution so that you do not have to go through each of the steps in Crop and Chop every time that you

need to process a new file.

9) “Enter the names of the files that you would like to process separated by a space.” Enter ‘CC20.ex1’.

10) At this point the screen will read “Processing File CC20.ex1” and subsequently 5 new files are

created because each time that the CC20.ex1 data was inside of the input data range (8929 to 9079 eV)

a new file was created containing data for one QXAFS scan.

11) The program exits. Now it is time to understand the output of CNC.

12) In the directory containing the CNC executable there will be a folder called Cuf. In this folder there

will be one folder named CC20.ex1 which will contain all of the data processed by CNC. If we had

processed multiple files there would have been multiple output folders each labeled with the name of

the input data files that were processed by CNC.

13) Inside of the folder CC20.ex1 there will be two folders, one labeled Noisy, and the other labeled

Smooth, and there will be two files EovsT.txt, and log.txt.

a) QXAD taken directly from the CC20.ex1 is contained within the folder Noisy. There are 6 data files

contained within Noisy which are labeled beginning with CC20.ex1. There is one file that is labeled

CC20.ex1.master.txt which contains all of the data inside of the 5 other files. These other files contain

data from each of the individual XANES scans in the QXANES run. The 5 scan files a named with a

number corresponding to the start time of that particular QANES scan which precedes .txt. b) Data

smoothed by CNC are contained within the folder Smooth. The data files there follow the same

nomenclature as those that are contained within Noisy with exception of the addition of “smooth” in

the file names. These files can be viewed with graphing software or Athena.

c) The file EovsT.txt is data that contains the Eo for each of the 5 scans as determined from the

transmission and fluorescence data. Note the first and last columns of data contain incorrect Eo values.

This is due to the fact that the 1st and 5th data files contain data from only a part of a XANES scan;

therefore, when CNC finds the Energy at which dMu/dE is a maximum it finds the wrong Eo. In your

independent studies use caution before presenting the data in EovT.txt. The values as dMu/dE are

calculated in CNC’s smoothing routine.

d) The log.txt file contains data that were used in the processing of CC20.ex1 and is important for

troubleshooting in your independent studies.

1.3 Example: The CC Agglomeration function and 3D Time Resolved Spectra

This example will teach you how to process multiple files which were collected successively using SCC

QXAFS data acquisition techniques with the Agglomeration function in CNC. After you successfully

execute CNC you will create a 3D plot of the QXAFS scans using Origin. In this section the symbol >>

leads you through the nested menu in Origin. For example the sequence File>>Open directs you to pull

down the File menu and select Open.

1) Complete steps 1 through 5 of Section 1.2.

2) “Would you like to process multiple files which are arranged in chronological order?” Enter ‘yes’ and

press enter on the keyboard. By entering yes you have called the Agglomeration function in CC.

3) “What would you like to name the directory and output files?” Enter ‘CuA’ and press enter. When the

Agglomeration function is called the output files will not contain the name of the input data files like the

example in section 1.2.

4) “How many files are you planning to process?” Enter ‘2’ and press enter. Three example files are

placed in the same folder as your CC executable.

5) “Enter the names of the files that you would like to process in chronological order and separated by a

space.” Enter ‘CC20.ex2 CC20.ex3’ and press enter. This is the same format that you would use if you

were planning on processing multiple files without calling the Agglomeration function.

6) The files CC20.ex2, and CC20.ex3 each contain 5 minutes of QXAFS data. After you press enter there

will be a brief pause and the prompt will display messages in the following format “File CC20.ex2

agglomerated”, etc. After the three files are agglomerated the file Agglomeration.txt is opened for

reading as indicated by the following prompt “Processing file ./CuA/Agglomeration.txt” The file

Agglomeration.txt contains all of the data that was in the files CC20.ex2 and CC20.ex3. Then you will see

the message “File# 1”, “File# 2”, ……….. “File# 40”. These prompts just show that 40 scans were collected

and processed by CNC. The program exits.

7) Open up the folder CuA located in the same directory as your CNC executable. Inside of the CuA

folder the setup is similar to that of the CNC output when Agglomeration is not called. Inside of CuA

there are two folders and three files which are Noisy, Smooth, Agglomeration.txt, EovsT.txt, and log.txt

respectively. a) The two folders Noisy, and Smooth, and the two files EovsT.txt, and log.txt are exactly

follow the same format as those created without the CNC Agglomeration function. See step 13 of

section 1.2 for details. b) The file Agglomeration.txt contains all of the spectral data from the files

CC20.ex2, and CC20.ex3 and the start time of CC20.ex2. It is an intermediate in the CNC processing

algorithm and generally will not be of any use elsewhere.

8) The file used to create a 3D time resolved spectral plot is located within CuA\Smooth\ and is named

CuA.master.smooth.txt. In this file you will notice that there are 9 columns: Energy, Time, Io, It, PIPS,

T_Mu, dT_Mu/dE, F_Mu, dF_Mu/dE. Where the T and F are for transmission and fluorescence

respectively. The important columns for this example are: Energy, Time, F_Mu, and dF_Mu/dE.

9) The subsequent instructions were developed based on OriginPro 7.5 software; your results may vary

depending on your version of software.

10) Open Origin. File>>Open find the directory where CuA.master.smooth.txt is located and change the

Files of type: tab along the bottom of the open window to read ASCII Data (*.dat;*.csv;*.txt). Select

CuA.master.smooth.txt and press open in the lower right hand screen of the open window.

11) Maximize the window that appears on the Origin screen and notice that there are the 9 columns

each of which is labeled by the name of the column in the ASCII file and a designation in parenthesize

which will be either an X or a Y. These correspond to the default axis that each column corresponds to in

a plot. The next step is to select the column labeled with Io, right click on it, and Set As>>Disregard.

Repeat these steps for the columns It, PIPS, TMu, dTMu/dE, and dFMu/dE.

12) Select the column FMu, right click on it, and Set As>>Z. Ensure that the column is highlighted and

Edit>>Convert to Matrix>>Random XYZ.

13) A window labeled Random XYZ gridding will pop up. In the upper right hand corner ensure that the

tab labeled Select Gridding Method is set to Renka-Cline and click on the OK button at the bottom of the

window.

14) A window labeled “Attention!” will display that “Duplicate XY pairs found, replace with mean Z

value.” click on the OK button.

15) With the Matrix1 screen active select Plot>>3D Color Map Surface. A plot of the matrix data will

appear. The edges will be distorted because the data in not in a uniform grid. No detailed features will

be present at this point because Origin plots by default in speed mode. This is so that each time a small

change to the figure is made Origin does not have to reload 10 MB of graphics.

16) Do not alter the data in the matrix; change the axis ranges so that the imaginary data is not

presented. This can be done by double clicking on the axis of interest and clicking on the “Scale” tab that

will be in the popup window. Set the x-axis range to 8940 to 9070, the y-axis range to 10 to 610 and the

z-axis range to 0.25 to 0.7.

17) Right click on the plot and select Plot Details. A window “Plot Details” will appear. On the left side of

the window there will be a tab “Layer1”, click on the “+” to the left of it this will open up a “Matrix1”

tab. Now on the right side of “Plot Details” window select the tab labeled “Grids” inside of the Grids tab

there will be a tab “Grid Line Width” in this tab, set the grid line width to 0.2.

18) With the Graph1 window active File>>Export Page. After a “Save As” window appears click the

“Save” button.

19) Open up your newly created file. It should be similar to Figure 2 below. Origin has a variety of other

features that will allow you to further tailor your image. However, this process will be left for your

independent studies.

Figure 2. The example figure produced from Section 1.3 example. Results in your independent studies

may vary and are strongly dependent upon the resolution of your data.

Section 2: Crop and Chop 2.0 Output

In the Crop N’ Chop 2.0 series software there are two main output systems. The output format is

dependent upon whether or not CNC has called the Agglomeration function. When CNC is run in

standard mode (Agglomeration is not called) there will be a series of folders inside of the user input

directory name which contain data corresponding to the file that the folder is named after. In

Agglomeration this system is not used because all data is processed from the file Agglomeration.txt and

therefore a series of folders are not required to organize the data within the user specified directory

name. The names of the files that are output when Agglomeration has been called by CNC are specified

by the directory where the data was stored because there is no longer a specific file that is associated

with the QXAFS scan. Effective use of the SCC data collection techniques and CNC can produce the data

which is present in Figure 3 at the end of this section.

2.1 The Noisy Folder

All QXAD that is collected using SCC techniques is inherently noisy because the integration times over

which signals are collected are on the order of 0.001 seconds. The Noisy folder is used as a storage point

for all of the data that is directly taken from the SCC QXAFS files. The noisy folder is located within the

user input directory name if Agglomeration was called and is located within the input file name if

Agglomeration was not called. In either case the format within the Noisy folder is identical.

Inside of the Noisy folder there are a series of files all of which are labeled by the following conventions.

The name of the file comes first and is followed by a period. After this a number is placed directly before

.txt. This number corresponds to the start time of this specific scan. This can be verified by opening a

given file and noting that the number with which a file is named corresponds to the first value of the

fourth column rounded down to the nearest integer value. Along with all of the files that contain a

number directly preceding the .txt extension there is a file which contains the .master.txt extension. This

file contains all of the data from the files in noisy and is useful to view the data in a 3D plot. (See section

1.3) The format inside of each of the files is exactly the same. In general there are 10 columns. The

following respectively lists there order and function.

1) Energy – calculated directly from Mono_Deg and Bragg’s law. Used to define the energy of x-rays

permitted to pass through the monochromator at every instant in the QXAFS scan.

2) Encoder – The raw signal converted to base 10 by the VME encoder from the base 2 signal output by

the Heidenhain encoder. This signal is collected by the SCC on-site QXAD collection computer and

corresponds to Bragg angle of the monochromator.

3) Mono_Deg – the Bragg angle of the monochromator calculated from the Encoder signal and the

model linear model of the Bragg angle as a function of the Encoder signal. (See Section 3.1 and 3.2)

4) RunTime – The time of the QXAFS scan offset such that the QXAD file was initialized is 0 by the SCC

data acquisition system is zero.

5) Io – The signal collected by the Io detector. Proportional to the incoming flux of x-ray photons

incident on the QXAFS sample.

6) It – The signal collected by the It detector. Proportional to the flux of x-ray photons transmitted

thought the QXAFS sample.

7) PIPS – The signal collected by the solid state pips detector. Proportional the flux of x-ray photons

emitted from the QXAFS sample by fluorescence, errors can be induced in this value due to heating of

PIPS detector or Compton scattering of the x-rays incident on the QXAFS scattering. Care should be

taken to reduce these errors are inherent to the fluorescence experiment.

8) Mu – The transmission coefficient – the log of Io divided by It.

9) PIPS/Io – The transmission coefficient calculated based on fluorescence data – PIPS/Io.

2.2 The Smooth Folder

The contents of the smooth folder are similar to those of the Noisy folder. The smooth files are named

with the root name followed by “.smooth.”. The one file has a .master.txt extension and the others have

the time at which the scan started as a extension followed by .txt. This makes it easy to differentiate

between data files which have been processed by CNC’s smoothing algorithm. The data in the

smoothing file depends on the number of points smoothed in CNC’s smoothing algorithm with

exception of the Energy and Time columns which are not smoothed by the SGS algorithm. These files are

kept raw because they allow for tracking of values between the noisy and the smoothed data. In general

an increase in window size of CNC’s smoothing algorithm will decrease the resolution of our data but

can increase the precision of each smoothed data point. (See Section 3.3)

The format inside of each of the files is exactly the same. In general there are 9 columns. The following

respectively lists there order and function.

1) Energy – The energy of the x-rays that were incident on the QXAFS sample at the center point of the

SGS window. The linear regression of smoothed data fitted vs. Energy.

2) Time – The time at which the center point of the SGS window was collected.

3) Io – The smoothed Io detector signal.

4) It – The smoothed It detector signal.

5) PIPS – The smoothed solid state PIPS detector signal.

6) T_Mu – The smoothed transmission coefficient.

7) dT_Mu/dE – The derivative of the transmission coefficient.

8) F_Mu – The smoothed transmission coefficient based on the fluorescence data.

9) dF_Mu/dE – The derivative of the transmission coefficient based on the fluorescence data.

2.3 The EovsT.txt File

The EovsT.txt file is used to generate time plots of the Eo progression. This is important if a QXAFS study

is taking place while the sample is being oxidized or reduced. When a sample is undergoing an in situ

oxidization electrons are being withdrawn from the atom under investigation. This results in core level

electrons which are deshieled from the nucleus of the atom. Thus, the electrostatic potential and

binding energy between the core level electrons and the nucleus increases. This is manifested in the

spectra by an increase in the Eo as defined by the energy at which dMu/dE is a maximum. In this case all

of the Eo is defined with the help of CC’s SGS algorithm which in the process of smoothing the data will.

It is suggested that this file be used to create kinetic plots of the in situ chemical transformations.

The output of the EovsT.txt file is contained within 6 columns. Three of these columns are devoted to Eo

data based on the transmission data and the following three are devoted to calculating the Eo data

based fluorescence. The first and last values contained in each of the columns should be checked

carefully because they may have collected the max derivative of Mu with respect to E from a partial

QXAFS scan that never collected data at the sample’s actual Eo.

2.4 The log.txt File

The log.txt file contains the calibration data that was used in the CC algorithm as well as the size of the

smoothing window used by the SGS algorithm, and notes on the author of CC. It is used for

troubleshooting in the case that CC does not execute well.

2.5 The Agglomeration.txt File

This file is output by the Agglomeration function and therefore is only present when Agglomeration is

called in CC. It contains data in the exact format of the input files except that the columns are labeled

with appropriate titles. These are Time, Io, It, PIPS, and encoder. The first five rows of the data file

contain one important piece of information. This piece of information is contained in the row that is

labeled “#Start Time:”. The value that is placed after this label is the time at which the first file in the

series of files that were agglomerated was created.

Figure 3. Data was on an in situ CuO to Cu(0) in-situ chemical transformation under a flow of 5% H2

collected at X18B processed with CNC and plotted with OriginPro 7.5. (a) Time resolved XANES collected

at a time resolution of 15 seconds per XANES scan. (b) A plot of dMu/dE based on fluorescence data.

Note the discontinuous shift in Eo. (c) Data collected via the SCC residual gas analyzer on the

concentration of the H2 and H2O in the reactor effluent stream. (d) A plot of the shift of dMu/dE max

bound by the condition that it occur at Energy

Section 3: The Crop and Chop Algorithm

3.1 Energy Calculation and Calibration

To determine the energy level that correlates to the Quick-XAFS data point the monochromator

diffraction angle must be known and applied to Bragg’s law (eq 1).

(1)

In Bragg’s law n is an integer representing the harmonic of electromagnetic radiation permitted to pass

through the monochromator crystal and can be assumed to be 1 if proper detuning procedures are used

(~30% at X18B), ? is the wavelength of the electromagnetic wave, d is the lattice spacing in the

monochromator crystal, and ? is the monochromator diffraction angle. At beam line X18B a Si(111)

double crystal monochromator with a lattice spacing of 3.1355Å is used to select x-rays from the

polychromatic synchrotron x-ray beam. After the wavelength of the x-ray is calculated it is a matter of

converting to energy via Plank’s constant and the speed of light (eq 2).

(2)

The Quick-XAFS setup at X18B measures the monochromator angle through an analogue to digital

converter at a resolution of 12 bits/0.01o. Therefore, Quick-XAFS files collected at X18B contain a signal

with a linear relationship to the monochromator angle. The slope of the angle as linear function of the

encoder signal is -409600/1o, a value which is dictated by the energy resolution of the analogue to

digital converter. The last degree of freedom in the linear fit of the encoder signal is the offset. However,

this value changes each time that the monochromator is cross referenced. Currently, the offset is

determined by finding the encoder value at Eo in a reference scan. The model of the Bragg angle (?) as a

function of the encoder value (enc) shown below where enco and ?o are the encoder value and Bragg

angle at Eo for a sample.

(3)

In order to use Quick-XAFS technology at X18B to the fullest extent a standard sample with a known Eo

should be scanned at each monochromator tangent arm setting, and immediately proceeding each

Quick-XAFS system start up or system crash.

3.2 Crop N’ Chop

The first step in the CC algorithm is to convert the digital signal from the VME encoder into energy. The

resulting energy varies as a sinusoidal function of time [Figure 3]. The program then starts at the first

point in the input data files and determines whether or not it is within the user input energy range. It

then implements this check to successive points. When CC counts that a specified number of

consecutive points - in the CC algorithm the variable Buffer controls this number - are within the energy

range of interest it initializes a file, resets its counter, and writes subsequent data to the new file. During

the writing process it is continuously searching for a number of consecutive points equal to Buffer that

occur outside of the energy range. When this occurs CC closes the file it was writing to and omits all data

that occurs until a number of consecutive points equal to Buffer are found to be within the energy range

of interest. At this point CC will initialize a new file and write subsequent data to the file. Etc.

As an example the data in Figure 3 is provided, the user input range of the spectra are 111 eV above and

39 eV below the edge energy of 8979 eV, an adequate range of data for XANES analysis. Starting at time

zero and continuing to the end of the run CC would omit roughly all data above 9090 eV and all data

below 8930 eV. While doing so it would create 5 files each containing one individual spectrum and one

master file containing all spectra. However, the first and the last file would only contain part of a

spectrum and therefore should be omitted from presentation.

Use of CC requires some knowledge of the data that is being processed. The most important pieces of

knowledge to have for the file splitting method are the upper and lower limits of your data. If the upper

or lower limits input into the CC algorithm were outside of the data range the output data files would

contain multiple spectra. For example, if the data in Figure 3 were processed with a lower limit set to 59

eV below the edge Crop Chop would only output 3 data files. You should model the energy range of your

data using the upper and lower limits of the monochromator angle. Also, the rates of change of the

monochromator angle can require new values of the CC algorithm variable Buffer.

Figure 4. Example quick-XAFS data collected at X18B. This is the encoder data contained within the file

CC20.ex1.

The smoothing algorithm in CC serves two purposes. The first of which is to smooth data collected with

SCC data acquisition techniques and the second is to provide dMu/dE as a function of the spectrum

energy. The CC smoothing algorithm operates by selecting a number of consecutive points and least

squares fitting the data to a line of the form in equation 4.

(4)

The fits that the CNC smoothing routing completes are Io, It, PIPS, Mu, and PIPS/Io as a function of

Energy. After the fit parameters a and b are determined the center point of the window of raw data is

estimated and written to the smooth output. CNC iterates this process until all data has been smoothed.

Values of b are also stored in the smooth output to model dMu/dE. Eo is then defined by the value at

which dMu/dE is a maximum.

In the CNC smoothing routine one parameter N, the number of data points smoothed, can have

dramatic effects on the efficiency of the CNC smoothing algorithm. N should be chosen such that the

energy range within N data points is less than 2 eV and so that N is greater than 5 data points. If the

former condition is not satisfied it will be difficult to determine accurately from CNC smoothing data the

correct value of Eo and many of the high frequency trending in the absorption coefficient will be

attenuated. The latter term is important because the data are noisy and therefore to obtain a precise

approximation of the center point of the window of data many points should be used to minimize the

noise contained within the smoothed data.

Section 4: Calibrating the Energy of a QXAS

1) Open up CC20.ex1 using plotting software of your choice. Note: Excel can only work with data that is

in less than 65536 rows and 256 columns. Excel’s 2D plots can not contain over 32,000 data points.

2) Create a plot of the encoder signal and the fluorescence vs. scan time. The encoder signal is contained

in column 5 and the fluorescence can be calculated by dividing column 4 by column 2. Time data is

contained in column 1.

3) The next step is to find the encoder value at Eo. In figure 4 the red point in the encoder data was used

to serve this purpose. Its value was ‘-4040478845710’ the Eo that it corresponds to is 8979 eV. Find you

own value of Eo. It should be within 6 orders of magnitude of the value above.

Figure 5. A plot that was used to determined the first guess of the encoder value at Eo. The actual

encoder point which was used for this purpose is in red.

4) Use CC to process CC20.ex1 and use your values of Eo and the encoder value at Eo as calibration

parameters.

5) Open up the EovsT.txt file to find what Eo was determined to be. Using the calibration data present in

this example the Eo of the sample was determined to be approximately 8988 eV. However, now the

time at which Eo occurred in the QXANES run is know.

6) The time at which Eo occurs should be roughly 11.842145 seconds in the first scan. Now the signal

form the encoder can be found at this time. This will correspond to the encoder value at Eo. To find this

encoder value open up the Noisy folder and open up the file named CC20.ex1.7.txt or the file which is

corresponds to the second XAFS scan in the QXAFS run. The encoder value was ‘-4040478840157’ which

is very close to the calibration data provided in Section 1.3.

7) The next step is to use the new encoder value to reprocess CC20.ex1 and see if the log.txt file

contains the proper values of Eo for the sample.

8) Steps 4 – 8 can be repeated to get a more precise calibration of the data but it is not recommended

that more than 1 or 2 repetitions are completed.

Improvements

In the future the following improvements to Crop N’ Chop software will be made.

1) A user input parameter that allows toggling between a first and second order polynomial to be used

in least squares fitting fro the smoothing routing.

2) A self calibrating routine that uses a standard quick-XANES or quick-EXAFS scan to determine the

Encoder value at Eo.

3) EXAFS data processing capacities: normalization, conversion to k-space, background fitting with cubic

splines to determine ?, Fourier transform into r-space. To make visualization of in-situ local coordination

changes simplified.

4) A graphical user interface (GUI).

Author

Nathan D. Hould

Research Assistant

Synchrotron Catalysis Consortium

NSLS - Brookhaven National Laboratory

Graduate Student

Department of Chemical Engineering

University of Delaware

http://www.yu.edu/scc/page.aspx?id=3998

E-mail: nhould@udel.edu