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CrysTBox cellViewer - visualization tool


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General information

This tool offers a user-friendly interactive interface showing the material from four different perspectives: direct atomic lattice (cell view), reciprocal lattice (diffraction view), stereographic projection (stereographic view) and inverse pole figure (IPF view). CellViewer provides two separate slots or views (left and right), each of which can be occupied by one of the four mentioned views. The user can therefore select such combination of two perspectives, which fits his needs. The tool can be used to visualize crystallographic planes, directions, their mutual position and orientation, it provides crystallographic calculator or a tool which helps to calculate the TEM holder tilts leading to the desired sample orientation.

Both, left and right views are interactive and interconnected: if you click at the diffraction spot in the Diffraction view for instance, a corresponding crystallographic plane is rendered into the 3D unit cell the Cell view or a mark is drawn at appropriate position in Stereographic view or IPF view. The amount of influence of one view on another can be adjusted by user. For example, the 3D unit cell in the Cell view can be freely rotated without affecting other views. If it is needed, however, the diffraction pattern in the diffraction view can be instantly updated or the pole in the stereographic view can be adjusted so it mathces the actual unit cell orientation.


Video >>

Input

Sample material

  • defined by unit cell
  • supported file formats: .CIF, .CELL
  • some materials are predefined, but user can specify arbitrary material (details...)
Results from diffractGUI (optional)
  • diffractGUI can pass the zone axis to cellViewer together with the information about the pattern orientation
  • a theoretical diffraction pattern and atomic lattice orientation shown in cellViewer should then exactly match the experimental diffractogram

Window description

cellViewer window

As mentioned above, the window has two views or slots (left and right), each of which can be occupied by cell view, diffraction view, stereographic view or IPF view. Content of both views can be selected via context menu (appears after a right click on the view) or using toolbar buttons , , and right below the main menu. Various properties and settings of individual views can be adjusted via main menu or more quickly via context menu and tabs in the bottom left part of the window. The tabs in the bottom right part of the windows show details about the selected crystallographic planes, directions, atoms, etc.

A detailed description of the graphical user interface follows.

Diffraction view
Diffraction view

This view shows a theoretical spot diffraction pattern. It can be activated by pressing the toolbar button . Individual diffraction spots are represented by disks. The disk size is derived from a structure factor. Crosses represent extremely weak or forbidden reflections. The sample does not need to be oriented in the exact zone axis and therefore, the diffraction condition is not perfectly met for certain diffraction spots. Those reflection then does not appear black, but they are shaded in grayscale - the darker the spot appears, the better satisfied diffraction condition is.

The diffraction view is interactive. User can click on the spots to see the details about corresponding plane in the Planes tab and to get the plane itself drawn into the Cell view. Basic settings can be adjusted in the context menu or in tab Diffraction view, all settings is available in the main menu.

The mouse actions available for this view are following:

Left click
Selects Plane 1 (blue).
Shift + Left click
Selects Plane 2 (red).
Right click
Shows the context menu.

Cell view
Cell view

This is an interactive view on the unit cell (or a broader atomic lattice) which can be activated via toolbar button . The atoms are represented as spheres coloured according to their element. User can zoom in, zoom out and rotate the unit cell using the toolbar buttons , and . As the cell is rotated, the actual crystallographic orientation can be seen in the top right corner. The actual orientation of the rotated lattice may or may not be instantly reflected in the Diffraction view or Stereographic view.

Similarly to the Diffraction view, user can select individual atoms using a mouse click. Selected atoms are highlighted and detailed information is shown in the Atoms tab. If only one atom is selected, its coordinates and element is stated there. In case of two atoms, information about vector between the atoms is printed. Three atoms generate a plane, which is described by normal vector and Miller plane indices. The plane is also rendered in the view. In case of four atoms, information about d-spacing is added.

The mouse actions available for this view are following:

Left click
Selects atom (green).
Shift + Left click / Ctrl+ Left click / Double Left click
Selects atom even if the rotation mode is turned on (toolbar button is highlighted).
Right click
Shows the context menu.

Stereographic view
Stereographic view

This view can be activated by the toolbar button . The view is quite intuitive. It offers a stereographic projection of selected planes and direction. The projection pole can be fixed or updated instantly to match the unit cell orientation in the Cell view. The grid can reflect either the plane or direction indices.

Clicking the plot, you can select planes or directions which are consequently shown in other views.

The mouse actions available for this view are following:

Left click
Selects Plane 1 (blue).
Shift + Left click
Selects Plane 2 (red).
Ctrl + Left click
Selects Direction 1 (blue).
Ctrl + Shift + Left click
Selects Direction 2 (red).
Right click
Shows the context menu.

IPF view
IPF view

This view is quite similar to the Stereographic view. It can be activated by the toolbar button . Compared to the Stereographic view, this view only covers a portion of the whole stereographic projection. The border of the shown area is given by three points, which can be set by user. The IPF triangle can be couloured. It can also be drawn into the Stereographic view or into the Cell view showing directly what the IPF stands for in the context of the unit cell.

Clicking the plot, you can select planes or directions which are consequently shown in other views.

The mouse actions available for this view are following:

Left click
Selects Plane 1 (blue).
Shift + Left click
Selects Plane 2 (red).
Ctrl + Left click
Selects Direction 1 (blue).
Ctrl + Shift + Left click
Selects Direction 2 (red).
Right click
Shows the context menu.

Sample tab
Sample tab

Material
Sample material can be specified using this field.
Zone axis
User can set desired zone axis here. Chenge of this field is always instantly reflected in both, left and right views.

Diffraction view tab
Diffraction view tab

This tab allows for a basic settings of Diffraction view. Advanced settings is available in the main menu.

Max. spot index
Here, you can set maximum spot (plane) index of diffraction spots plotted in the Diffraction view.
Max. plane dev
This field specifies how tollerant the Diffraction view is to declination of actual orientation from the perfect zone axis. The higher is the value, the higher declination from the ideal zone axis is allowed to draw the spot in the diffractogram. Note, that the declination is reflected in the darkness of respective diffraction spot - the higher is the declination, the brighter is the spot.
View range
Specifies X and Y axes limits of the diffractogram.
Update zone axis from Cell view
If checked, the diffractogram is redrawn instantly as the unit cell is rotated in the Cell view.

Cell view tab
Cell view tab

Basic settings of the Cell view can be done in this tab. Advanced settings is available in the main menu.

Lattice span
Controls how many atoms are shown in the Cell view. Zero denotes "human friendly" unit cell (e.g. whole hexagon in case of HCP structure). Numbers higher or equal to one stand for a block of NxNxN "true" unit cells. Higher number of atoms may result in increased hardware requirements.
Rel. at. radius
Using the Relative atomic radius, you can set size of spheres representig the atoms as percent of distance between the two nearest atoms in the structure. In other words, value of 100 means, that two nearest atoms in the unit cell will touch each other. Numbers higher than 100 make some of the atoms intersect with each other, while Numbers lower than 100 make the Cell view sparser and easier to see through.
Surface complexity
Each atom visualization (sphere) consists of many flat faces. Number of the faces can be set here. Higher numbers make the atoms smoother. Higher number of faces may result in an increased hardware requirements.
Preserve viewpoint
The Cell view viewpoint is reset (to given zone axis orientation) after aplying some Cell view changes (such as Surface complexity, Rel. at. radius and so on). This checkbox allows to preserve the unit cell orientation set by the user (e.g. by rotation, TEM holder tilting etc.).
Transparent planes
This checkbox makes the planes in the Cell view transparent, so that the atoms behind them can still be seen.

Stereographic view tab
Stereographic view tab

Here you can control the Stereographic view. Advanced settings is available in the main menu.

Pole
Miller indices of the direction corresponding to the projection pole can be set here.
Click selects
This radio button determines whether the left mouse click selects a direction or plane. The other one can be selected with Ctrl.
Grid shows
Here it can be specified, whether the grid reflects directions or plane normals.
Update pole from cell view
This checkbox allows the projection pole and upper direction to be automatically updated if the unit cell is rotated.
Show theoretical reflections
If checked, the theoretical planes (corresponding to the reflections in the diffractogram) are shown in the stereographic projection. Max. spot index from Diffraction tab applies here.
Show IPF
Appearance of the IPF in the Stereographic view can be controlled here.

IPF view tab
IPF view tab

The IPF can be adjusted here. Advanced settings is available in the main menu.

Pole
The IPF pole (corresponds to the bottom left/right corner) is specified here as a direction vector in Miller indices.
Right/Left corner
The side corner of the IPF triangle is set here as a direction vector in Miller indices.
Upper corner
The upper corner of the IPF triangle is defined in this field as a direction vector in Miller indices.
Click selects
This radio button determines whether the left mouse click selects a direction or plane. The other one can be selected with Ctrl.
Show theoretical reflections
If checked, the theoretical planes (corresponding to the reflections in the diffractogram) are shown in the stereographic projection. Max. spot index from Diffraction tab applies here.
Coloured IPF
This checkbox switches between white and coloured IPF.

Planes tab
Planes tab

This tab states details about the planes either given by a mouse click to the views or entered manually using fields Plane 1 and Plane 2 in this panel.

Plane 1
This field states the Miller indices of Plane 1 (the blue one). It can be filled manually or automatically after clicking to the Diffraction view, Stereo view and IPF view.
Plane 2
This field states the Miller indices of Plane 2 (the red one). It can be filled manually or automatically after clicking to the Diffraction view, Stereo view and IPF view.
d-spacing
D-spacings of both planes Plane 1 and Plane 2 are stated here.
Interplanar angle
If both planes, Plane 1 and Plane 2, are specified, an angle between them is printed in here.

Atoms tab
Atoms tab

Details about atoms selected by the mouse-click in the Cell view are mentioned here. As you click on particular atom, its coordinates (in Miller indices) are added to the field Atoms. Atomic coordinates can also be entered manually, separating individual atoms with semicolon. The detais about the selection depend on how many atoms are selected:

  • one atom - element, atom coordinates (Miller and Cartesian)
  • two atoms - elements, direction of vector between the two atoms (Miller and Cartesian) and their distance (Miller and Cartesian)
  • three atoms - elements, plane normal vector (in Miller and Cartesian coordinates)
  • four atoms - elements, plane normal vector (in Miller and Cartesian coordinates) and d-spacing

Directions tab
Directions tab

This tab states details about the crystallographic directions either given by a mouse click to the views or entered manually using fields Direction 1 and Direction 2 in this panel.

Vector 1
This field states the Miller indices of Direction 1 (the blue one). It can be filled manually or automatically after clicking to the Stereo view and IPF view.
Vector 2
This field states the Miller indices of Direction 2 (the red one). It can be filled manually or automatically after clicking to the Stereo view and IPF view.
Length
Lengths of Direction 1 and Direction 2 are stated here.
Angle between vectors
If both directions, Direction 1 and Direction 2, are specified, an angle between them is printed in here.

Calculator tab
Calculator tab

This tab offers a crystallographic calculator. After selecting the quantity to be calculated in the pop-up menu, the descriptions of required parameters appear next to the text fields. When all the inputs are set correctly, the results are printed at the right hand side of the tab.

Supported calculations involve:

  • conversion between Miller and Bravais notation for planes and directions
  • conversion between Miller and Cartesian coordinate system for planes and directions
  • enumeration of interplanar and interdirectional angles
  • d-spacing enumeration and assignment
  • calculation of structure factor, atomic scattering amplitude or extinction distance

Export tab
Export tab

Some of the crystallographic quantities can be exported to a text file using this tab.

Input parameters
This panel is used to set the calculation inputs - mainly the range of Miller indices of enumerated planes. Some calculations also require the acceleration voltage.
Exported quantities
Quantities exported to the table are specified here using the checkboxes.
Export file
In this tab, you can specify character separating individual values in the table using Separator pop-up menu. Then, you can launch the exporting procedure pressing the button Export. Status of the procedure is stated bellow.

Holder calibration tab
Holder calibration tab

This tool allows you to simulate the TEM sample holder. Some basic calibration is required for this purpose. Holder visualization on the right hand side of the tab should help the user to check, whether all the values have been set correctly.

Holder azimuth
This field specifies orientation of the holder with respect to the sample orientation currently shown in the Cell view. This value is an angle between alpha tilt axis and Y (vertical) axis in degrees.
Direction of positive rotation angles
These pop-up menus allow you to specify whether the positive angles tilt the holder to the right or left for alpha tilt and upwards or downwards for beta tilt (watching from the holder handle towards the holder tip).
Tlts leading to shown unit cell orientation
These fields are used to set alpha and beta tilt (in degrees) corresponding to the sample orientation as currently shown in the Cell viewer.
Calibrate
If all previously mentioned values are set and the holder visualization agrees with the reality, calibration can be confirmed pressing this button.

Holder navigator tab
Holder navigator tab

This panel allows you to simulate TEM holder tilts. It can also calculate holder tilts required to get the sample to desired orientation.
Note: If the fields in this tab are not enabled, please perform the calibration using the Holder calibration tab

Tilt
Text fileds Alpha and Beta (in degrees) can be used to tilt the sample in the Cell view and to see corresponding diffraction pattern in the Diffraction view (if the checkbox Update zone axis from cell view in panel Diffraction view is check-marked).
Zone finder
This panel allows you to find the alpha and beta tilts leading to the desired zone axis. Ususally, the TEM holder tilts are limited to a certain range. Therefore, you can select whether you want to be navigated exactly to the zone axis which is stated in the text field (radio button Exactly as stated) or rather to such crystallographically equivalent zone axis, which is nearest to the actual sample orientation (radio button Nearest equiv.) or to the crystallographically equivalent zone axis with the least holder tilts (radio button Least-tilt equiv.).

Author contact

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