Set up and run files

Initial setup of a GudrunX file

The GudrunX GUI looks very similar to Gudrun, with the functions for adding panels and files, running the program and plotting the data all operating in the same way.  

When GudrunX is opened, it defaults to displaying information from the XRDstartup_windows.txt file.  This contains information for the instrument, beam, normalisation and sample background and should be set up correctly to let you get started.  

Instrument panel: This panel is primarily used to give Gudrun the various files it needs to run, and the location of the input file (in C:\GudrunX or C:\GudrunX\run for example) and the location of the raw data files.  GudrunX requires three files from the GudrunX folder to run

  • Cross section file:          CrossSec_XCOM.txt, 
  • Form factor file:              f0_WaasKirf.txt 
  • Compton scattering file: CrossSec_Compton_Bayuzi.txt
Instrument panel

Instrument panel
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Beam panel: Nothing should need to be changed on this panel, although you should ensure that the bremsstralung file is correctly located.

Normalisation panel: This is the first panel which you will have to edit to ensure the data GudrunX outputs is in the form you require.  Two options for the sharpening are given, Sum(cifi2) or Sum(cifi)2.  You should choose the method which you prefer.  If in doubt, consult your instrument scientist.

The Breit-Dirac factor should be a number between 2 and 3.  It has limited impact on the resultant S(Q), so leave as 2.5 unless you have a good reason for altering it.  You can also change the method of normalisation, but the Krogh-Moe/Norman method is recommended.

Normalisation panel

Normalisation panel
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Sample background panel:  This is the final panel which will be opened on starting GudrunX.  An initial sample background file will be given, but you should alter this to the empty diffractometer file given to you after your experiment.  You should reduce the background factor to somewhere between 0.85 and 0.95.

Background panel

Background panel
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Once you are happy with the settings in the first four panels, the sample and sample holder panels can be added through Edit→'Insert SAMPLE' or 'Insert CONTAINER'.  These tabs can then be renamed through EditRename.

Although the sample tab should appear in the list before the container tab, the latter is much simpler to edit.  Both panels require:

  • .XRDML file names (the location of the files should be set in the instrument panel)
  • Sample composition
    • Element symbol,
    • Form factor symbol- usually the element symbol unless you wish to use ionic form factors,
    • Composition - amount of each element either as a fraction (0.333 and 0.667) or formula unit (1 and 2).
    • q and delta - always zero
  • Inner and outer dimension of the material
  • Sample height, 2 cm unless an unusual XRD configuration was used
  • Effective density and tweak factor
  • Total cross section- select 'Tables'

Container Panel: When setting up the container information, the inner and outer radius of the capillary is required.  The first value is the radius of the capillary, and the second includes the thickness of the capillary wall.  For a 0.5mm capillary supplied by ISIS the values would be 0.025 and 0.026.  

The density of the capillary is well known, but it should be considered that when the capillary is full, some scattering from the capillary will be lost.  To account for this the container tweak factor should be increased from 1.0.  This will have the effect of reducing the amount scattering from the container removed from the sample data.  As a guide, this value should be between 1.2 and1.4.  

Inspection of the amount of signal in T(r) at 1.6 Å will give a good guide to how the tweak factor should be altered.  See related links for more information.

Container panel

Container panel
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 Sample panel: The sample panel also requires an effective density for your sample.  Ideally a measurement of this should be made while loading the capillary but if this was not done, and good starting point would be to enter the actual sample density and set the tweak factor to ~2 (50% packing).  Depending on the sample the packing fraction could be lower than 25%.

When adding a new sample tab, make sure that the number of iterations is greater than 1, otherwise F(Q) will not alter. 

GudrunX is not as straightforward to use as Gudrun, and some experimentation with the parameters should be expected to get a good fit.  The majority of this parameters are in the sample panel and they are:

  • Effective density,
  • Flourescence - a particular problem for elements in the same row as Ag,
  • Multiple scattering,
  • Polarisation - should be left as 0,
  • Compton scattering - should be left as 1,
  • Bremstralung - should have a number around 0.55

 

Sample panel

Sample panel
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Once you have some initial values in GudrunX, you should first check that all the files needed can be found Run → 'Check files exist' and then the program can be started Run → 'Run GudrunX'.  GudrunX will then go through several iterations to scale the experimental data with the calculated form factor for the sample, after the various corrections have been applied.  Once the program has finished, the newly calculated Sample calibration factor will be given on the sample panel, and the output files can be viewed.

 

 It can take a lot of work to get your data looking right, patience is required!  Information on how to view and improve the outputs for GudrunX is given on the viewing outputs page.

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