Powder X-Ray Diffraction - Data Collection, Analysis and Report

Rachel Kusnic, Matthias Zeller

Part 1: Preparation of Sample

1a) Powder Sample

The powder is to be packed into the sample cup tightly so that the powder is level

with the sample cup. If the powder does not pack tightly, vaseline or wax can be

used to help hold the powder in place.

1b) Solid Sample

The solid is to be held in place in the middle of the sample cup by using e.g. a

piece of wax. The top of the sample should be even and smooth and level with

the top of the sample cup.

Part 2: Data Collection

2a) Create a folder for yourself in the folder I:\data\ . Copy one of the default dql files

from I:\data\default dql\ into the folder just created

2b) Place your sample cup in a free position in the 9-sample sample-changer

2c) Open or switch to the program XRD Commander. You will be using this program to

set up and monitor your data collection.

The interface of the XRD commander has four sub-layers: Adjust, Jobs,

Geometry, and Details. You can switch between the layouts via the tabs at the

lower left corner of the layout. You will need to use Jobs and Geometry.

Geometry and Details are more monitoring purposes only.

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2d) JOB measurement

Switch to Jobs. From the menu select Create Jobs:

In the new window fill in the values for your sample. Provide your sample

position, your sample ID, the location of the parameter (dql) file you are going to

use, and the name and location of the output ("raw") file. Use the feature to

access the windows navigator.

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Data should be saved in your subfolder of I:\data\.

Important: The software does not create a path that does not exist (it creates the

raw file). It also does not recognize folder names with spaces. In both cases it will

perform the measurement but will not safe the data!

You can edit the default dql file if needed. Place the cursor in the parameter file

box and click to open the dql editor ("XRD Wizard").

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Check that the values displayed agree with the ones given in the above figure.

You may change any of the following values: Start (only larger than 15 degrees!),

Stop, Step size, No. of Steps, Time/Step. The Changing any of the values will

automatically update the Total Scan Time. You may also switch on or off the

rotation. No other values are to be edited!

Loosely packed powders should not be rotated. If you do rotate a loose powder

you will be billed for any repairs to the motors necessary resulting from

spilled sample! Densely packed ones and solid materials (e.g. a piece of metal)

can be rotated. Rotating does homogenize anisotropy within the plane of the

sample holder (and thus improves the data quality if you are not interested in this

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 anisotropy). It does not average anisotropy perpendicular to the sample holder

direction (see "handling of preferred orientation" in the data workup section).

When done either save the file (do not overwrite the default dql files in

I:\data\default dql\) or save it under a new name (you need to reload the file in the

Jobs Editor). Close the XRD wizard.

Back in the Jobs Editor click on to begin your measurement or to add

it to the queue (if another sample is already running). You can load several jobs at

once in the Jobs Editor. They will be measured in the order they were submitted

to the diffractometer. The Jobs interface will list the active sample and all recently

measured and pending samples.

You can halt a running sample via Jobs, Halt Active Measurement, e.g. to load

more samples into the sample changer (do not open the diffractometer doors with

a sample running!). Restart the interrupted measurement by highlighting it in the

Jobs list and invoking the button.

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Part 3: Measurement Monitoring

After starting your measurement you can monitor the process in the Adjust sub-

layer of the XRD Commander. With the Vantec detector, an area detector, data

will not show up for several minutes but angles will be shown to move.

Part 4: Data Workup

4a) Using EVA

Open the Eva program .

Go to File, Import, Scan File. The screen will look like this:

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If the background is large a background correction might be necessary. In the

Toolbox click on Backgnd., then Replace.

The next step will be to find the peaks. Click on PeakSearch. The software

attempts to assign lines with the peaks. You can adjust the number of lines using

the scrollbar in the lower left corner of the Toolbox. When satisfied click on

Make Diff.

Now you can try to match your data to an entry in the database of known

compounds. In the main Eva window click on the Search/Match button. The

screen may look like this:

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In the Search/Match window select the elements that maybe present in your

sample (highlight green ). You may also unselect elements that are for sure not

present (highlight red). Start the search. The program will usually find a whole

range of possible hits, but upon visual inspections only very few are really

possible hits. The two figures below show an example of a possible hit and an

example of a mismatch.

In the first figure (the possible match) all lines of the pattern from the database

(blue) do line up with the experimental pattern (red lines). Some of the

experimental lines do not fit to the database entry, which indicates that there

might be a second or third compound present (mixture of compounds).

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The second pattern shows no match for all database lines and thus the database

entry cannot be a match for the experimental pattern.

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After assigning the peaks to one or more compounds from the database (which is

of course only possible for known compounds listed in the database) you should

delete the not-fits in the Toolbox and select the matched with a checkmark. The

result, in this case a mixture of three compounds (NiO, Tl2O3 and BaCO3) may

look like this:

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For your report export the file as a pdf file in the following way: Print the page as

an Adobe PDF file. Select the Cute PDF printer, select Properties, Page Setup,

Landscape. Print the file. When prompted save the pdf file in your folder in

I:\data\. Save the pdf file on your USB drive. It might look like the following

example:

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Part 3: Using TOPAS

The program TOPAS has a range of advanced features such as Peak Shape and Unit Cell

Fitting as well as Rietveld Refinement. Even with quickly collected data that are

not quite suitable for a full refinement you can still get useful information from a

Rietveld refinement such as refined unit cell parameters, rough ratios of the

crystalline components in the sample, or preferred orientation of the crystallites in

your sample. It is also a better proof of identity than just a line fit, and hkl values

for the diffraction pattern are calculated automatically.

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3a) Obtaining the CIF files

A quick Rietveld analysis is easiest if your compound has a diffraction pattern with

known unit cell and atom positions (Indexing, solving and refining an unknown

pattern is still an extremely challenging task and is usually part of a PhD or post

PhD level class). After identifying the components of your sample via Eva you

need to find and export the CIF files (Crystallographic Information File) from a

suitable database. For inorganic compounds this is the "Inorganic Crystal

Structure Database" of the "Fachinformationszentrum Karlsruhe". A copy is

installed on the powder XRD computer, the shortcut on the screen is named

"FindIt"

Several search modes are available. The most commonly used ones are by mineral name

or by chemical formula. In the chemical formula search (default, shown below)

select "Exclusive AND" to avoid excessive numbers of hits.

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To access the mineral search interface select "Reference" in the window header, then

check Mineral Name/Group to obtain an alphabetical listing.

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Click search to obtain a listing of possible hits. You need to select the most suitable hit

for your purpose. Your selection needs to be

- chemically identical to the compound you are looking for

- the same crystal phase as the desired compound (if known)

- atom positions need to be reported and no errors should be listed

- the collection temperature and pressure should be close to ambient

In the example from above (NiO, Tl2O3 and BaCO3) the results for BaCO3 (Witherite)

looks as follows.

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To export the CIF file check your choice, then "export selected long view" as shown

above. Choose the option CIF for saving and give the file a suitable name (e.g.

Witherite.cif). Save the file in a new folder and repeat the process for all

compounds found in your sample.

3b) Topas

Open Topas.

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Editing all parameters needed for a Rietveld refinement is outside the scope of this

maual. Instead open a preexisting project. Use the default Topas project located at

I\data\DefaultTopas\DefaultTopas.pro

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Save the project under a different name in the folder where your cif files are located.

Then replace the raw file in the default project by your raw file via a right mouse

click on the raw file as shown below ("Replace Scan Data").

Then import the cif files via a right mouse click on the raw file ("Load CIF(s)"). Repeat

the process for all components. The cif files will be listed below the raw file.

At this point, if the X-Ray pattern is not displayed in the main lower window "unzoom" it

as shown below.

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In the default settings for the imported cif files the unit cell parameters would not be

refined. Usually there are small differences between the unit cell parameters in cif

files (they might have been obtained for higher accuracy at lower temperature,

resulting in slightly contracted unit cell axis). You thus need to change the code

from "Fix" to "Refine" to obtain a better fit as shown below.

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Save the project. Then export the INP file (input file) as shown below.

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Set the INP file:

Then click the black triangle in the upper right quarter of the interface. The refinement

should start. Often however the cif files have slight errors or incompatibilities.

Common are oxidation states not allowed in Topas, e.g. C+4 for carbon. An error

message such as the following will pop up.

Correct the oxidation state by highlighting "Sites" in the compound with the problem.

Then change the oxidation state as shown below.

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Shown below are two results from a refinement for the mixture NiO, Tl2O3 and BaCO3.

The fit is shown in the lower main window. The upper graph is the experimental

pattern overlaid with the calculated pattern (contributions from individual

compounds can be highlighted by clicking on the compound names to the right).

The grey line below is the difference between experiment and fit. The lowest

section shows the Miller indices for all refined compounds. You can obtain the

numbers of individual indices by moving the mouse atop of the triangles.

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The fit in the upper example (same dataset is obviously much worse than the lower one).

The difference resulted from a wrong cif file initially used for Witherite obtained

at high temperature (over 1000 K).

Another problems that may arise is preferred orientation of the crystallites in your

sample. A typical indicator for this problem is that the intensities of reflections do

not fit the experimental pattern well while the peak positions do. If this is the case

identify the peaks that have the largest difference between experimental and

calculated pattern and note its Miller index. Often the plane associated with this

peak is preferentially oriented (e.g. if the crystallites are thin plates that were

pressed in the sample cup so that they come to lie all parallel atop of one another.

The plane of the plates is often identical or perpendicular to the plane associated

with the Miller plane showing the largest difference). Under the structure listing

of the compound with this problem select "Preferred Orientation" and edit the hkl

values obtained. It your choice is correct the refinement fit should improve

significantly.

If you need to repeat the refinement you need to

- delete any additional raw files added to the upper left box

- make any changes needed

- save the project file

- re-export the INP file

- rerun the refinement

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When a satisfactory result is obtained you need to export the graphical fit and the results

from the refinement for your report. Export the file as a pdf file in the following

way: Click File, then. The following interface will pop up.

Select your choice (either print to pdf or make a metafile or bitmap). Save the file in your

folder in I:\data\.

To obtain the numerical values of the refinement open the output file in notepad:

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The file will look shown below. You may want to write down the six R values and the

goodness of fit. For each compound also may want to note the unit cell parameters for a

comparison with the values in the input cif file.

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For your records you may want to save the following files:

- The linepattern fit obtained in EVA.

- The compounds identified, including chemical formula, mineral name (if available),

crystallographic space and unit cell parameters as given in the cif file.

- The Rietveld fit obtained in Topas including the ratio obtained for the compounds

present.

- The six R values, the goodness of fit and the unit cell parameters obtained in Topas.

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