This section describes the different features of the polyxsim graphical user interface.
The workbench refers to the main window of the polyxsim. It serves as the container of the different views. Views can be resized by :
Moving the separators between views,
Maximised by double clicking on the title bar of view
Detached from the workbench by right clicking on the title bar and selected « Detached »
Clicking on the minimise or maximise buttons of a view
Reset the workbench to its default aspect by selecting « Edit -> Reset Perspective ». This will return the workbench to its original aspect with one window for the PolyXSim Input view. Use this option if you are confused about the windows open and want to restore the workbench to its original layout.
To return to the PolyXSim perspective (input view) click on the PolyXSim icon in the Perspective cool bar or select PolyXSim – Open PolyXSim Perspective
The PolyXSim user interface is implemented in one input view. The other views (ImageView, TransformationView, Preprocessor etc.) are part of the Fable interface and are there to assist the user to look at files or analyse polycrystalline data (real or simulated). The input file parameters are described in the help on input file. The graphical user interface is a graphical frontend to the python implementation. It can be used to load an input file, display the parameters, modify them, save them and run the simulator and display and analyse the results.
The PolyXSim Input View consists of at least 6 tabbed windows. The tabs are :
Files
Crystal Phases
Sample
Reflections
Instrumental
Detector
The Files tab displays the input file last loaded, the output files to generate and the contents of the input file. To display the full contents of the input file double click on the PolyXSim Input view tab. You will should see something like this :
If you modify the contents of the input file then the Save as button becomes enabled and you can save the modified contents of the Input file.
NOTE : the contents displayed is the contents of the input file as read, it does NOT (yet) reflect the contents of the input tabs if they have been modified.
PolyXSim simulates samples with multiple crystal phases. The number of phases and their description are specified in the Crystal Phases tab.
Phases can be specified as cif or pdb files or using their unit cell and space group. Click on the Crystal Phases tab and select the type of input you want e.g. Read structure from file (cif or pdb) :
The cif/pdb structure can be displayed using the Jmol viewer (by
clicking on the icon
) :
Choose space group and specify unit cell (currently only inputting space group numbers are allowed, space group names can however be specified in the input file) :
The Sample input tab displays parameters relative to the sample like size and number of grains to simulate :
NOTE : the total number of grains MUST be the same as the sum of the grains in all phases. If not PolyXSim will print and error message and not run.
The Reflections input tab displays the parameters on how the reflection intensities are generated and the shape of the diffraction peaks :
NOTE : the constant input parameter displayed in the graphical user interface is not (yet) passed on to the simulator.
The Instrumental input tab displays the input parameters relative to the xray instrument e.g. Wavelenght, beam position, rotation axis, steps per image rotation etc. :
The Detector input tab displays the parameters relevant for the detector like distance to sample, size, orientation, tilt, point spread function etc :