QUICK XAFS MANUAL. Andrew Friedman 1 and Elie Horowitz 2 Yeshiva University, New York, NY 10033

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1 QUICK XAFS MANUAL Andrew Friedman 1 and Elie Horowitz 2 Yeshiva University, New York, NY Introduction: Quick XAFS (QXAFS) is a mode of collecting fast (1 s per scan or better) XAFS measurements, to study in situ processes (e.g., reduction/oxidation reactions, nucleation and growth of nanoparticles, etc.). This manual is intended for scientists unfamiliar with basics of QXAFS who are planning to incorporate this method in their synchrotron research. This document consists of (I) the general description of the method, (II) details of the experimental setup, (III) a detailed, step-by-step, instruction for data acquisition and (IV) an example of a data acquisition session. I. Method/Technique: According to Bragg s Law of Diffraction the wavelength of the incident radiation to a given plane of a sample s crystalline structure can be measured. The formula is n λ = 2d sinθ where n is an integer corresponding to the harmonic of the incident wave, λ is the wavelength of x-rays as well as moving protons, neutrons and electrons, d is the distance of the spacing between the planes in the atomic lattice, and θ is the angle between the incident ray and the scattering planes. Essentially as theta changes so does the wavelength of the incident beam of electromagnetic radiation (and obviously its scattering planes), and the wavelength can be translated to a particular value of energy by the equation E = hc / λ where h is Plank s constant, J/s or ev/s. The EXAFS method interprets the wavelengths of these incident rays and scattering planes as particular values of energy and illustrates that on the connected computer during an energy scan of a particular sample. In standard EXAFS the monochromator will periodically move slightly, halt, and then collect data at that angle, thereby causing the experimenter to lose out on the data between the 1 jaywilljr21@aol.com 2 milinasa@aol.com

2 initial and final oxidation states of the sample due to this abrupt starting and stopping of the monochromator. In quick EXAFS, a cam and pivot arm are coupled to the EXAFS motor and monochromator allowing for continuous rapid motion of the machinery, enabling the collection of continuous data throughout the reaction. Essentially, the cam holes and pivot points on the pivot arm allow for monochromator to oscillate anywhere between ± 0.15 and ± 2.25 and enable the collection of data on the fly. The monochromator will continuously oscillate back and forth altering its position, and consequently the theta value described above in a continuous fashion. This continuity enables the experimenter to visualize through an exorbitant number of data points taken by the EXAFS machinery the chemical & physical environment of the atom(s) he is interested in during the reaction itself instead of being limited to the initial and final states therein. II. Experimental Setup ASSEMBLY (Changing from EXAFS motor setup to Quick EXAFS motor): 1 Turn off Heidenhain readout box. 2 Clamp the perforated metal board and remove the springs 3 Unscrew straight screws attaching ball and then unscrew ball 4 Unscrew ¼ turn each of 2 screws in monochromator arm with Allen keys 5 Unscrew screws of rectangular bar to detach the EXAFS motor. 6- Remove and unscrew black cable connecting monochromator to readout box.

3 7- Connect female component cable to the disconnected cable in step six. 8- Connect the remaining black cable to the readout box. 9- Line up QEXAFS motor with separate rectangular metal piece resting on its indent. Then screw in the mounted motor and rectangular metal bar. 10- Place the wheel behind the metal board and screw it in with 4 screws. 11- Fasten the brass pivot parallel to the monochromator arm at either the middle (B) or left hole (A) depending on the experimental setup. 12- Screw in 3 screws to attach the silver, rhombus cam to monochromator arm, 2 on the upper corners and one screw on top. 13- Screw in black backed screw between the pivot into the desired hole depending on the experimental setup. 14- Pull O-ring around the metal disc and the motor cylinder. 15- Unscrew clamp 16- Turn on the readout machine and press enter. 17- Pull lever of monochromator until readout passes 360 degrees and then continue to get a rough estimate of the lower angle of the angle range desired by experimenter. 18 Fine tune the angle to value desired by alternately screwing/unscrewing the screws in monochromator rear. 19 Rotate metal disc of quick exafs setup until arrive at lowest angle value possible. 20 Re-adjust the angle value at this low point to the low-angle value desired with steps 17 & Plug in power supply to power strip Disassembly of Quick EXAFS back to Standard EXAFS 1 Unplug power supply to power strip 2 Turn off readout machine 3 Remove O-ring pulled around the metal disc and motor cylinder 4 Unscrew black-backed screw inserted into the numbered hole 5 Unscrew 3 screws and metal piece attached to monochromator arm 6 Unscrew and remove brass pivot arm

4 7 Unscrew and remove quick exafs motor with metal bar 8 Unscrew and remove quick exafs wheel & attached ball under arm 9 Unscrew black cable from readout box 10 Disconnect black plugs attached to each other and plug male component into read out box 11 Screw in ball and then secure it with 4 straight screws into top and bottom holes on either side of metal arm 12 Line up and screw in at 4 corners the standard EXAFS motor to the metal board 13 Attach 1 spring on either side of the 2 straight screws on the motor Standard EXAFS setup Lever Mono Arm Metal Board EXAFS Motor

5 Springs Ball 1 of 4 straight screws 2 screws inside monochromator for readout angle fine-tuning adjustment

6 Quick EXAFS Parts Metal Disc Numbered Wheel Rectangular Metal Piece Silver Rhombus Cam Brass Pivot Arm Point A Pivot Arm Point B O-Ring Blackbacked Screw Quick EXAFS motor

7 III. Data acquisition: A. Motor Speed Adjustment 1 - Click on the Konsole icon on the bottom left of the desktop 2 Type ls and press enter 3 Type cd dcmotor and press enter 4 Type python dcmotor.py and press enter 5 Adjust motor speed in pop-up window as desired B. Collecting Data 1 Enter Password to access QEXAFS computer 2 Select Konsole icon on desktop 3 At prompt x18b type in ls to bring up directories/subdirectories and press enter 4 Type cd qexafs ( cd stands for change directory) and press enter 5 Type ls and press enter 6 Type cd gui, press enter, then ls, and then press enter again to open directories within graphical qexafs interface 7 Type python mac.py and press enter to initiate graphical user interface (gui) program 8 In upper left corner is window of Dir, a data storage directory where user can enter whichever directory experimenter desires (i.e. Click lower left corner icon on Konsole window to open another terminal window) 9 - type pwd at prompt and press enter to show the present working directory 10 - Type cd /home/data/qe and press enter to go to directory most often used to store user data 11 Type ls and press enter to show subdirectories where different users have previously stored data 12 - Type mkdir andrew and press enter to create new subdirectory titled andrew (example of user name) 13 - Enter /home/data/qe/andrew into Dir window of gui at upper left corner and press enter to enable data storage for current user

8 14 - Name data file as qexafs.dat in data file window of gui and in adjacent window enter sample extension for naming data file and press enter (i.e. Au.001 for first scan of a gold sample) 15 - Insure that hardware, beam, motors are all aligned and prepared for data acquisition 16 - Click Take Data (By default, the QEXAFS machinery will collect 60,000 data points in 30 seconds time 17 - To check that data was entered into appropriate directory type cd andrew into Konsole 18 - Type ls l and press enter to provide the long form of the file content in the directory (as opposed to just the name of the file had one simply entered ls as mentioned above) containing the size of the file in bytes as well as the date and time of data taken 19 - To take another data file select Take Data again and the file extension will be automatically increased by an increment of one 20 - To take multiple data files sequentially enter the desired number of scans into the loop window and then select Take Data 21 - To analyze a particular region of the data move the cursor to a given position on the graph on the screen left click and hold the mouse down to drag a box around the data points to be examined 22 - To zoom back out click the right mouse key 23 - To toggle the visibility of a particular signal s data points (It, If, Ir etc) click on the corresponding signal s button on the graph s screen 24 - To plot a composite curve, select the plot table tab at the bottom of the screen (instead of the default timing tab and select desired signal s in signal A and the Signal B (i.e. To see Io/It in the first row of the plot table select Io in the signal A column and It in the signal B column) 25 - The user can toggle in the signal C column between time and encoder as options for x coordinate of plot. If encoder is selected, then in the X-unit column one can opt for the x- coordinate to be represented/graphed as a function of either the encoder, energy, k-unit, or angle. 26 The user can toggle the scale (log/linear) or colors of a given plot in columns four and six, respectively, of the plot table. Motor Adjustment 1 - Click on the Konsole icon on the bottom left of the desktp

9 2 Type ls and press enter 3 Type cd dcmotor and press enter 4 Type python dcmotor.py and press enter 5 Adjust motor speed in pop-up window as desired QEXAFS Transfer of Data from Unix machine to Internet folder which can then be accessed by user to subsequently download his data onto a personal computer: 1 Go to user s folder on the Unix machine 2 Type ftp ftp.nsls-user.bnl.gov and press enter 3 For user name type anonymous; Enter password 4 type cd X18B and press enter (Commands are case sensitive) 5 Type binary and press enter (transfers in binary format) 6 Type prompt and press enter (turns prompt off to dump all files) 7 Type mput * and press enter (dumps all files to the server) 8 Type bye and press enter (exits program) 9 The data will now be available for a 5-day period after which it will be erased 10 To access this data on personal computer type in above hyperlink (ftp.nsls-user.bnl.gov) select beamline data was taken on (in aforementioned steps it would be X18B) select and save data to hard drive/usb Alternate Method of Data Transfer: 1 If necessary, the data can be transferred directly to external hard drive through USB port (To use this capability contact particular beamline s personnel for assistance)