Current version 3.8.0 (2020-07)

Tutorial: explore the silicon crystal

Author: Damien Caliste

This tutorial requires at least version 3.4.

This tutorial is made to explore the box duplication capability and the different aspects of planes. Some binding functionalities will also be used. It is focussed on the silicon whose primitive lattice is an FCC one with two atoms. The equivalent non-primitive cubic cell has 8 atoms.

Create the primitive lattice

We can create the input file using the ASCII file format. In this format, the FCC lattice has a particular definition:

# V_Sim ASCII FCC box definition for a silicon distance of 2.35
        3.83959          1.9198         3.32518
         1.9198         1.10839         3.13501

Then comes the atoms coordinates:

# Box contains 2 nodes.
#  | 2 nodes for element 'Si'.
               0               0               0 Si
          1.9198         1.10839        0.783753 Si

If the ETSF plug-in is available, one can also use the following input file which has a more common definition for an FCC lattice. This file must be converted to binary data with the ncgen executable from NetCDF.

From version 3.5, one can also use the following ASCII file, using keywords:

# V_Sim ASCII format for primitive cell of silicon
  3.83959 3.83959 3.83959
  60      60      60
#keyword: angdeg, reduced, angstroem
        0.00    0.00    0.00  Si
        0.25    0.25    0.25  Si

Expand the box to create a cristal

Available since 3.4.

It is possible to interact with the box in many ways, like changing the colour of the bounding box, but also for geometrical properties like periodic translations or duplication. We will use the latter here to expand our silicon crystal to more than two atoms.

Draw planes

V_Sim can draw one or several planes, using (in particular) the crystalographic directions. Planes can then be used to clamp the rendering area and hide atoms. We will use this capability here to for particular surfaces in silicon. Planes are defined by their normal vectors and their distance from origin. One has also to choose a colour for the plane.

Isolate a cubic silicon cell

We will use six planes to isolate a cubic silicon cell. To do this, we need to find the directions in the FCC lattice basis set that will give a cubic basis set. In the following, node ids can differ if the node expansion has been modified from the one suggested at the beginning.

Change the basis set and export file

From version 3.5, one can modify the basis set by pointing on atoms to define a new basis set.

After, one can export to a file, using the small SaveAs icon on the bottom left of the rendering window and choose a text exportation (either ASCII or XYZ).