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CrysTBox - ifaceViewer step by step


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ifaceViewer step by step

Since the ifaceViewer (see GUI below) is a visualization tool, there is no strict workflow here. Still, some hint of how the tool can be controlled, can be found below.

1 - Select sample material

Compared to other CrysTBox tools which all require only one sample material to be specified, the ifaceViewer is intended to visualize two phases and therefore two materials must be set. Materials of Phase 1 and Phase 2 can be specified either in the Phase 1 / Phase 2 panel next to the unit cell visualization or in the Phase 1 / Phase 2 tab in bottom part of the window. Details about material database and selection can be found here.

In our example, let us keep the default Aluminium for both phases.

2 - Interface setup

The interface is defined by the following three aspects: misorientation between both phases, position of one atom shared by both phases and orientation of the interfacial plane dividing the two phases All those parameters can be set in the tab Interface setup (see above).

The misorientation can be specified in many ways by controls located below the text Misorientation given by:

  • Parallel planes and parellel dirs - this way requires the user to specify Miller indices of one plane in phase 1 and another in phase 2, so that the both planes are mutually parallel. In addition to the pair of planes, a pair of directions parallel in both phases must be provided.
  • Parallel dirs and parallel dirs - this option is rather similar to the previous one. Another pair of directions is just used instead of the pair of planes. Again, Miller indices are used to define the directions.
  • Axis and angle - rotation axis and angle is defined for each phase resulting in the final misorientation. The axis is defined in Miller indices and the angle in degrees.
  • Euler angles - this allows the user to define rotation of each phase via Euler angles in degrees
  • Rotation matrix - here the user can specify 3x3 rotation matrix for each phase.
  • CSL - the misorientation parameters can also be set to comply with a Coincidence Site Lattice (CSL). CSLs are available for cubic, hexagonal and HCP structures. They are defined by Sigma value and by one of possible angle-axis pairs (available in the pop-up menus).

Common point specifies an atomic position shared by both mutually misoriented phases. For each phase, the point is defined using Miller indices below the text Common point.

Interfacial plane defines the boundary between the two phases. It is defined by the common point (see above) and then either by two other points incident with the plane or by the plane indices. The prefered way should be selected in the pop-up menu below the text Boundary plane given by.

The plane indices can be specified in the coordinate system of either phase. Similarly, the two incident points (atoms) defining the plane can belong to phase 1, phase 2 or both.

3 - Interface visualization

The interface visualization can be controled in the tab labeled Interface view (see above). Four visualization modes (see the image below) are available and can be selected via the pop-up menu in top left corner of the tab:

  • Unit cells - in this mode, each of the two phases is only represented by a single unit cell. Both unit cells are put together, so that they share the Common point as set in the previous step.
  • Unit cells (wire model) - this mode is rather similar to the previous one. Instead of being represented by individual atoms, the unit cells are reduced to a wire model.
  • Bulk - unlike the previous modes, this one allows rendering of a wider volume. The atoms are rendered so that they fill a cube a of predefined volume (8 nm3 by default). The slider Visible volume enables the user to reduce the rendered volume to a slice parallel to the interface plane. This allows for a visualization of anything between a single-atom thick layer of atoms intersecting the interface plane and the full volume of the predefined cube.
  • Cross section - this mode is similar to the previous one. The only difference is, that the Visible volume slider slices the rendered volume prependicularly to the interface plane. Azimuth of the slicing plane can be controled by the Point of view slider. This allows the user to create an illustrative cross-sections of the interface. Please note, that even though you need to visualize a single-atom slice, the Slice thickness should be reasonably high (not zero), otherwise, too few atoms can be displayed.

Unit cells Unit cells as wire model Bulk Cross section

A number of other visualization options is available. Atom colour can be changed for either phase and for CSL. The atoms not belonging to the CSL may be made transparent or even invisible allowing for a better insight into the CSL, etc.

4 - Visualization of planes and directions

Crystallographic directions and planes can be visualized via Direction & Plane tab. The direction or plane can be specified by its Miller indices in a coordinate frame of either phase. Alternatively, the user can specify the plane or direction by selecting incident atoms with a mouse click. To do so, press the toggle button Select with mouse and click either into the unit cell or to interface visualization. Note, that if you have enabled the rotation mode, you need to hold Ctrl key while clicking to select the atom. After selecting proper number of atoms (two for direction, three for plane) corresponding plane or direction is shown in the selected colour (black by default). The selected plane or direction is updated each time a new atom has been selected untill the toggle button is released.

Author contact

If you have any questions, offers or comments, please feel free to contact me:
Miloslav Klinger
e-mail: klingeratpost [dot] cz