USE OF THE X-RAY DIFFRACTION UNIT
FIFTH DRAFT
This document outlines the use of the X-ray diffraction (XRD) unit in the Geology Department. The system
consists of a Norelco generator, a Philips goniometer, a CrystalLogic interface controlling the goniometer
and the acquisition of data, and software obtained from the Chinese Academy of Physics for the processing
of the data. The detector for the XRD consists of a NaI iodide crystal coupled to a photomultiplier tube.
The arm of the goniometer has a grating that filters out Cu K radiation from the copper tube normally used.
It is the user's responsibility to familiarize himself/herself with the contents of this document before using
the instrument. Careless errors can damage the instrument but might be hazardous to the user. The X-ray
generator is a source of ionizing radiation!
SAMPLE PREPARATION
Thoroughly grind the sample. The acquisition of accurate intensities from the powder method assumes a
random orientation of crystallites. If the well is not ground well and the crystals in the sample are too large,
this ideal is not reached. Our present unit does not rotate the sample.
The sample can be applied to a special (expensive) Phillip mount, a microscope slide, or a Bakelite cylinder.
Chemistry students will use the microscope slide; geologists prefer to use the Bakelite cylinder.
Sample Preparation Using a Microscope Slide (Chem 160 Method)
In the case of the microscope slide, one could create a glycerine mull of the sample and apply it to a 1” x 3”
microscope slide whose length is reduced to yield a slide with the dimensions of 25.4 mm x 46 mm.
Uniformly apply the mull over the area 25.4 mm x 30 mm. Other groups have used double sided tape. One
side of the tape could be attached to the slide and the pulverized sample could be applied to the adhesive
surface. A mull would not be required in this case. In Chemistry 160, we shall employ a third method using
a uniformly greased slide. It has given much improved results.
The determination of the structure of your compound rests on both the positions and the intensities of the Xray reflections. The analysis of the intensities requires that the crystallites in your sample have random
orientations. Results obtained using the method described in the lab manual indicate that this assumption is
not satisfied. Presumably, the high pressure in the press partially orients the crystallites. The following
method appears to give greatly improved results.
1) Carefully and fully grind the sample in a mortar and pestle. Adding ca. 10-20 ml of acetone to the sample
appears to aid the process of pulverizing the sample.
2) Decant off the acetone and allow the sample to dry.
3) The sample may form clumps. Break up the clumps with a spatula or a glass rod.
4) The sample will be mounted on a modified glass microscope slide. A regular microscope slide is cut to
yield a slide with dimensions (w x l) of 25.0 mm versus 35.0 mm.
a) Uniformly cover 20.0 mm of the length of the slide with a thin film of stopcock grease.
A second slide may assist in the application of the layer.
b) Gently drop small portions of your powdered sample onto the greased area of the slide.
Gently tap the side of the slide to knock off the sample that does not adhere to the grease.
c) Repeat step 4c until the slide is uniformly coated with your sample.
d) Note that 15.0 mm of the slide is not coated with the sample. This uncoated section is
used to mount the slide in the diffractometer.
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Sample Preparation Using Bakelite (method used by geologists)
Usually the sample will be applied to a pressed Bakelite cylinder. This procedure will therefore be followed
in most cases. You will use a press and a stainless-steel die. Use the die with a 1” diameter. The die set has
the following components:
1) an outer die
2) a stainless steel cylindrical insert
3) the inner die
4) an aluminum sleeve
5) piston.
First assemble the unit. Insert the cylindrical insert, polished side up, in the outer die. Then insert the inner
die and finally the aluminum sleeve. As noted above, ground the sample very carefully. Add sufficient
sample so that it will uniformly cover the bottom of the die assembly. Tap the die assembly to spread out
the sample. Tamp the sample with an aluminum tamper that fits into the brass sleeve. Carefully remove the
tamper and check for a uniform layer of the sample. Hold the inner stainless-steel die and carefully remove
the aluminum sleeve. Add 3 heaping 1/4 teaspoons of Bakelite. Carefully insert the stainless-steel piston.
Transfer the assembled die assembly to the table of the press. Turn on the power. Engage the clutch and
slowly crank on the compressor control clockwise until the piston of the press engages. Then increase the
pressure to 5 Ton and hold it for one minute. Release the pressure, slowly for the last ton of pressure. Turn
the compressor control counterclockwise until the pressure drops to zero; then give the control another
counterclockwise turn. Disengage the clutch. Dissemble the die assembly and remove the sample.
Scrupulously clean the components of the die assembly. Residues of ionic salts can severely corrode the
components of the die!
PREPARATION OF THE X-RAY GENERATOR
1) The generator has a total-elapsed time counter. Record the time (starting time) in the log for the unit.
2) Power is supplied to the Norelco generator through a Voltage regulator located on the floor that produces
a clean, constant voltage. Check that the supply is on. It should not be turned off and should be found in the
ON state.
2) Open the valve for the water supply that cools the X-ray tube. The valve is located on the wall. The lab
is crowded so be careful not to hit the goniometer as you approach the valve. The previous user should have
moved the goniometer out of harm's way to the 2 = 80 position. If it is in a lowered position and
susceptible to attack, consider using the POWDER software as described below to raise it up. The valve is
closed when the yellow lever is perpendicular to the wall. (The water pressure should be at least 45 psig; the
generator checks this parameter and a microswitch in the generator won’t close if the water pressure is too
low.)
3) Check that the VOLTAGE and CURRENT KNOBS ON THE Norelco generator are in the full
counterclockwise position. Also check that the current switch is in the MINIMUM MA position. Confirm
that the shutters for the x-ray ports are closed.
4) Start the flow of the cooling water by pushing the START button on the front panel of the generator.
Make sure that you hear the flow of water.
5) Start the generation of X-rays by pressing the ON button above the water START button. This button
stays pushed in when engaged and the red warning light is illuminated. The light should go on within ca. 30
second. Wait ca. 5 min. for the generator to warm up. X-rays are now being generated although the flux is
low when the Voltage and current are low.
6) Check that the copper X-ray tube is installed. The Voltage and current values provided below apply to
this tube. If a different tube is installed, check with the Geology Department. The Voltage and current
settings appropriate for a copper tube might burn out other, e.g. iron, tubes.
7) Slowly adjust the Voltage of the supply to 35 kV.
8) Turn the current switch from MINIMUM MA to OPERATE. The Voltage will drop below 35 kV. Do
not re-adjust the Voltage back to 35 kV.
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9) Slowly increase the current to 20 ma. Again, the Voltage will continue to drop but do not re-adjust the
Voltage back to 35 kV. The X-ray tube is now producing a high flux of X-rays.
INSERTION OF THE SAMPLE
1) Confirm that the shutters are closed! Control the shutters via the program.
2) Open the enclosure by sliding it to the right.
3) If your sample is applied to a pressed Bakelite cylinder (normal situation), load the sample into the
aluminum holder and tighten down the springs.
4) Loosen the nut holding the circular plate on the mount.
5) Rotate the plate counterclockwise and remove it.
6) Remove any sample in the mount.
7) Using a wedge, e.g. a small screwdriver, depress the tight spring clip and insert the sample, e.g. the slide
or the Bakelite cylinder) face up. Be careful not to push the sample in too far..
8) Re-attach the circular chamber plate. To do this, hold the lever against the shutter button so that the
plastic knob will not restrict the cover. Rotate the cover clockwise about 20º and tighten the central nut.
You may have to push the nut in slightly to secure the sample chamber door.
9) Close the enclosure by sliding it to the left. You may have to apply gentle pressure to fully close it and
close the microswitch.
CONTROL OF THE SHUTTER
The shutter mechanism is now interfaced with the computer. Please only open the shutter via computer
control. You may damage the electronic interface if you open the shutter manually. Port 2 which you will
be using feeds the Philips powder goniometer. Port 4 is permanently closed. Ports 1 and 3 are available for
alternate goniometers and for a powder camera.
The following information is provided for use of the technician. Do not fiddle with the control knob.
A control knob for each port has 4 positions:
1) OFF, the shutter is closed. Turning the knob to this position will close the shutter.
2) , the shutter is open permanently.
3) A, the shutter is open for A hours (0A4 hours. A set by a dial).
4) B, the shutter is open for B hours (0B23 hours, B set by a dial)
To open the shutter with the computer:
1)Make sure that the computer, and all the hardware is turned on; the black CrystalLogic control box has to
be turned on before the computer or the program will not communicate properly with the interface.
2) Start the POWDER program by double clicking on the POWDER.exe icon, which displays the NaCl unit
cell.
3) Click on Manual from the top menu line. A new window will appear that enables direct control of the
goniometer and shutter (Figure 2). The shutter can be opened by clicking on the Shutter button. Go back to
the main window POWDER by clicking Cancel.
(To manually open a shutter, (NOT for student use!!): turn the control knob to , A, or B. In the case of
the A or B settings, set the appropriate time. Press the SHUTTER OPEN button. The shutter will open and
a light will go on. If the bulb for the light burns out, the shutter will close.)
The shutter is associated with variable slits. The slits are varied under program control to provide a constant
illuminating area for all values of 2. This was not the case with older constant-slit units with resulting
systematic errors in intensities.
ACQUISITION OF DATA
As mentioned before, the system is controlled by an interface designed by CrystalLogic under CrytstalLogic
software. Separate software, PowderX, is used to analyze the raw data. If you used the computer to open
the shutters then you can proceed to the procedure explained below. If you manually opened the shutters
then make sure that the computer, and all the hardware is turned on; the black CrystalLogic control box
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found to the right of the PC has to be turned on before starting the software. Initiate the control software by
clicking on the POWDER.exe icon which displays the NaCl unit cell.
The POWDER window (Figure 1) has four sections, starting from the top:
1) the menu line
2) a panel with colorless fields for inputting control parameters, e.g. the initial value of 2, and green fields
for displaying the status of the instrument, e.g. the current value of 2.
3) the diffraction pattern, either directly measured or downloaded from a dataset
4) a panel for providing information that is appended to a file that is created for each run. None of the
parameters entered in this panel are measured directly, e.g. the wavelength of the X-rays. The file button in
the bottom panel is used to provide the path, file name, and format of the file that is created.
The following simple procedure will yield a useful dataset.
1) Turn on the CrystalLogic control box first or the program will not communicate properly with the
interfacl
2) Start the POWDER program by double clicking on the POWDER.exe icon.
3) Click on the File button in the buttom panel and provide the format for the dataset to be produced (I
recommend the default .dat format), the path (consider saving your data on a 3.5" diskette so the hard drive
is not cluttered), and the file name for your data.
4) Check that the current setting of the monochromator is synchronized with the interface. Click on Manual
in the top menu line. A new window will appear that enables direct control of the goniometer (Figure 2).
The sample changer and slit functions in the window do not function. The program's measurement of the
current setting of the goniometer (2 in degrees) is displayed in a box. Read the actual setting of the
goniometer. It should agree with the number in the box. If not, enter the actual value in the box and click
on the Define button. A mistake at this point will introduce a serious systematic error! You can also change
the position of the goniometer with the meter. Enter the value of 2 in degrees and click on Drive. The
number which you select must fall in the range 0<2<125. Don't even come close to the limits. There is
no reason to. The goniometer will move to the new position. To exit from the manual window, click on
Cancel.
4) Provide the control parameters in the colorless (white) fields in the top panel:
a) The initial value of 2 in degrees. This must be a positive, non-zero number. Consider for your
first run a value of 5.0. There is no value in running lower than 5 as the intensity data in this regime
is dominated by specular reflection.
b) The final value of 2 in degrees. This must be less than 120. The goniometer has stop which
prevent 2 from falling outside these limits but the stop does not always function. However, if a
limit is reached, the goniometer must be reset manually by a technician so please do not tempt fate.
Steer well clear of the limits. In the vast majority of experiments, there is no reason to come close.
c) the goniometer step size in degrees. The position of the goniometer is controlled by a stepping
motor and this parameter is the increment in 2. Optimal resolution is achieved with 0.02 and there
is no value is running with a smaller value. However, higher resolution incurs longer run times. For
a survey run, consider a step size of 0.1.
d) the count time in seconds. For each setting of the goniometer, counts are accumulated over count
time seconds. Consider 1 s in your first run. Increase the value if the signal-to-noise ratio is too low.
Recall that the standard deviation of the mean is inversely proportional to the count time.
5) Insert your sample if you have not already done so and open the shutter on port 2.
6) Start the run by clicking on the Start button on the right side of the lower panel. The light in the PC
window will turn from green to red and the shutter should open with an audible click. The goniometer
should stop at each setting for the count time. If it does not and is rapidly stepped through its angular range,
immediately stop the run by clicking on Abort before the goniometer reaches the stoop and jams. Consult
the technician or your instructor if this happens. Also seek assistance if the shutter does not open.
The detector is interfaced to a multi-channel analyzer. An X-ray photon passing through the NaI can
produce a cascade of visible photons. The number of visible photons produced per X-ray photon is
proportional to the energy of the X-ray photon. The electronics in effect a histogram of the number of
detected X-ray photons versus the energy of the photons. For each setting of the goniometer, the total count
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of all X-ray photons falling in a certain range is passed to the computer and the result is displayed in one of
the green fields in the top panel and the diffraction pattern plotted in the center of the window. The range of
useful data (channels 200 to 900) was determined via the scdw.exe routine when the instrument was
installed. The graphical display of the results is automatically scaled . However, buttons on the left of the
graph permit the user to expand or reduce the scaling. The results are displayed on the screen and are stored
in the file specified in step (3). The green fields in the top panel display the number of counts at each setting
of the goniometer and the time remaining for the run in seconds. You should notice that the data will be
written to disk as the run proceeds. Windows is not a real-time operating system and writing to disk takes
priority over control of the goniometer.
7) When the run has finished, close the shutter, this will automatically be done if the shutter was opened
through the software. Consider making a second copy of your data by clicking on File and then Save As.
Save As rd appears not to work properly. The program has very few features for the analysis of the results.
A second program is used for that purpose.
ANALYSIS OF THE DATA
A flexible analysis program has been provided by Professor Cheng Dong of the Institute of Physics, Chinese
Academy of Sciences, Beijing, People's Republic of China. A manual in Microsoft Word rtf format,
Pxusere.rtf, can be found in the folder c:\xray-china.
1) Preparation of the ASCII file produced by POWDER. Professor Dong's program can read X-ray datasets
in a number of formats. However, the POWDER .dat format is not on his list. However, a POWDER .dat
file can be easily converted to an acceptable format, e.g. .xrd. In the following example, the file to be edited
has the name test_WES.dat. A file in the POWDER .rd format can be converted to a Sietronics .cpi format
that can be read by PowderX. However, the creation of a .xrd file from a .dat file is much simpler and will
be described here.
a) Make a copy of the original file with the extension .xrd. That is, the copy would be test_WES.xrd.
b) Open the copy using Microsoft Notepad or Word. The POWDER .dat format consists of a
multiline header followed by a data section. In the data section, each line contains the value of 2 in
degrees and the number of counts. In editing the copy, strip off all lines of the header except for the
first one, which reads: Sample Sample. This line which can be up to 80 characters long is used to
identify the sample. This header line, e.g. sample junkite, should be followed by a new line which is
the number of values of 2. Use a left-hand justified integer format. That is, no decimal points and
no spaces at the left. This new line is immediately followed by the lines of data, one for each value of
2. Save the file. You are now ready to use PowderX.
3) Start the PowderX program by clicking on the PowderX icon on the Windows desktop. Windows should
allow the user to run concurrent sessions of both POWDER and PowderX. The PowderX window is shown
in Figure 1 attached to the end of this document.
4) Open a file for analysis by clicking on File and then Import Data. Select the .xrd format. Figure 3
displays the PowderX window and the diffraction pattern for sodalite. The sodalite2.dat file provided as a
test file with POWDER was modified as described in step (1) and imported into PowderX. PowderX
assumes that the X-ray generator uses a copper tube.
5) Follow these steps to generate a list of the peaks.
a) Click on Peak in the menu line and then on Simple Peak in the submenu.
b) A box for the input of the parameters, Select Points and Intensity Limit, appears. You may wish to
choose the default values at first. Click on Show to see the consequences of your choice. The
selected peaks are marked by a small tic mark. To remove weaker peaks from consideration, increase
the value of Intensity Limit and/or Select Points. Decrease the value(s) to include weaker peaks.
Once you are satisfied with the selection, click on OK.
c) A Wavelength box now appears in which you select the X-ray source (the default is copper), mode
of dispersion (angular dispersion, our case, is the default), and the radiation used. Unless one uses
routines in PowderX to strip off contributions from Cu K 2 radiation, click on average. The correct
wavelength, 1.54178 Å, appears in the box. This number can be changed. Click on OK when you are
finished.
d) A new menu appears for the input of the path and file name of the ASCII (txt) file where the results
can be stored.
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e) Finally, a window appears with the results. One can print the results directly using the File
command in the menu line of the printer. The table includes for each peak the values of 2, d, peak
intensity, peak area, and FWHM.
PowderX provides a variety of routines to select peaks and to filter the data. The most useful of the lot is
probably the baseline correction routine (click on Process, then Background, and finally Sonnerveld).
However, experience with the sodalite test file indicates that they be used with caution.
SHUTDOWN
1) Close the shutter and slide the enclosure back.
2) Remove the sample from the chamber. RE-attach the chamber cover and close the enclosure.
3) Turn the current control knob counterclockwise to the stop position.
4) Turn the current switch from the OPERATE to the MINIMUM MA position.
5) Turn the Voltage knob counterclockwise until snug.
6) Hit the OFF button to stop the generation of X-rays.
7) Wait until the Voltage drops to zero. If the unit has been used for several hours, wait 10 minutes to insure
complete cooling of the X-ray tube.
8) Then, push the STOP button to turn off cooling water to the machine.,
9) Verify that the current and Voltage knows are off (fully counterclockwise).
10) Close the valve for the cooling water. The valve is closed when the yellow lever is perpendicular to the
wall.
11) Do not turn off the Voltage regulator for the X-ray generator.
12) Record the elapsed time in the log for the system.
13) Manually set the goniometer to 80. This will move it out of the way. Click on Manual in the
command line to bring up the manual control window (Figure 2). Enter the value of 2 and click on Drive.
Click on Cancel to exit and return to the main window.
13) Exit from the POWDER program by clicking on File and then Exit
useXRD.doc
3 Sep. 2001, revised 5, 17 Sep. 2001, 12 Jan. 2004, WES
Revised: Jan 16, 2003 by Geol Technician
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Figure 1. Main window of POWDER.
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Figure 2. Manual Control Window of POWDER.
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Figure 3. powderX Window. The sodalite dataset is displayed.