Crystal definition

Lattice

The unit cell is defined by the length of its three edges a, b et c and by the three angles α, β et γ between two vertices.

Depending upon the selected Bravais lattice, some of these parameters are fixed or dependents. Only independent parameters may be changed, entries corresponding to constant or dependent values are disabled.

Lengths must be given in picometers and angles are expressed in degrees.

Atoms

Every atom in the unit cell must be defined. Necessary parameters are:

x, y, z

x, y et z are the atom coordinates in the cell given respective to the cell size. For instance, the triplet 0, 0, 0 puts the atom at the cell vertices and if the threee coordinates ere equal to 0.5, the atom will rest at the center of the cell.

Élément

Clicking this button allows to change the selected chemical element or to select one is there is no label in the button. Selection is made inside the dialog box containing the periodic table of the elements (see the section called Selection of a chemical element)

In this software version, choosing an element is optional. In future versions, it might be used to access a database.

Radius

The atom is figured as a sphere whose radius is expressed in picometers in the same way as the cell size. While the radius is null, no atom can be added in the list.

Color

The color used to paint the sphere representing the atom is selected by clicking on the button and picking a color in the dialog box that pops.

The number of visible atoms depends on the model size (see the section called Size) and on cleavages (see the section called Cleavages).

Buttons at bottom right are used to manage the atoms list:

Bonds and lines

Every bond or line present in the model must be defined. Necessary parameters are:

Coordinates

x, y et z are the coordinates of the two ends of the line or bond. These parameters are only available for bonds and some lines. They must be given in cell coordinates for the two ends in the respective entries.

Radius

The radius of the cylinder used to figure the bond or line must be given in pm as is the cell size. While the radius is null, nothing can be added in the list.

Color

The color of the cylinder used to figure the bond or line is selected by clicking on the button and picking a color in the dialog box that pops.

Type

Lines, figured as cylinders, are of several types:

  • Cell edges: if this type is selected, a cylinder is added for each cell edge.

  • Diagonals: cylinders are added that join opposite vertices in the cell.

  • Medians:cylinders are added that join opposite face centers in the cell.

  • Bonds and lines: a cylinder is added to join the points whose coordinates are given in the appropriate entries. A Cylinder is added for every visible cell.

  • Not duplicated lines : a cylinder is added to join the points whose coordinates are given in the appropriate entries. Only one cylinder is added whathever the visible cells number is.

Bonds and lines effectively visible depend on model size (see the section called Size) and cleavages (see the section called Cleavages). If one end of the cylinder lies outside of the visible part of the model, the cylinder will be hidden.

Buttons at bottom right are used to manage the bonds and lines list:

Size

Model size is expressed as relative cell coordinates. The necessary values are maximums and minimums of the three coordinates

It is also possible to cut the model using cleavages (see the section called Cleavages) if one wishes to limit the visible part by planes others than those corresponding to a constant value of a coordinate.

Cleavages

Cleavages are used to hide from the views atoms from planes with a orientation fixed by the Miller indices h, k and l.

If x, y and z are the atomic coordinates relative to the cell, Miller indices define planes as all the points such that hx + ky + lz is a constant. By instance, in a cubic network, (111) planes are perpendicular to the diagonal of the cubic cell going from vertex 0,0,0 to vertex 1,1,1.

Each define cleavage will hide the chosen number of planes beginning from the greatest value for hx + ky + lz that is present in the model. To remove planes from the other side of the model, signs of h, k and l must be reversed.

There is no need to define cleavages of (100), (010) or (001) planes because the same effect may be obtained more easily by changing the size of the model (see below the section called Size).

When a cleavage is defined, the model is zoomed so that it fills the view as explained elsewhere (see the section called View). The Fixed model size button allows to keep remaining atoms at the same place in the view which may be useful to chain pictures in a presentation.

Buttons at bottom right are used to manage the cleavages list: