Tutorial: explore the silicon crystal

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

• Run V_Sim and visualise the file.
• In the "Elements" panel, decrease the radius of silicon atoms to 0.625 with the spin button.
• One can add bindings between silicon. To do this, check the box near the "Pairs" button on the main command panel. The bindings are drawn depending on type and distance criterions. Select the Si-Si binding line and change the minimum and maximum distance values between which pairs are rendered. There should be a binding for distances around 2.35 for the specified input file (one can also use the "auto-set" button).
• We can directly measure the distance between our two atoms. Look at the bottom of the rendering window, the status bar states that we can right-click and shift-right-click on atoms. The former select an atom and the latter is used to select a reference. Pick an atom with shift-right-click and select the second one with a simple right-click: the measured distance between the reference and the selected atom is drawn. It is indeed 2.35.

Expand the box to create a cristal

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.

• Select the "Box" panel and check the "Expand node" box.
• At that time, the box is not extend (expansion is 0 in the three directions). Increase the dx value with the mouse wheel or using the keyboard.
• Do the same for the dy and dz values until an expansion of 1.5 is reached for each. We have now 128 atoms in the rendered area (see the little information at the bottom of this window).
• Look at the crystal and try to find the peculiar crystalographic orientations of silicon like the [110] channels or the [111] hexagonal motif. If the perspective is too important, decrease it with shift mouse-wheel.
• The camera moves can be disturbing while looking for [100] direction for instance. This due to the fact that the default observation mode is made to keep the z direction up, and in our case, the z direction is not the [001] direction of the cubic lattice. To change the mode to a more versatile one, click on the "Mouse actions" button of the command panel and select the walker mode (top right).

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.

• Select the "Planes" panel and check the use box.
• Click on the "+" button to add a plane. It will use the values printed in the spin buttons of the panel, namely (1;1;1) at distance 4.7 here. The drawn plane is delimited by the bounding box of the rendered file (expanded here).
• Change the normal values and see how the plane is affected. The spin buttons gives the normal in the orthogonal V_Sim coordinates, not the box coordinates. So, in our case, a [010] plane is not orthogonal to the box y vector. To enter normals in box coordinates, click on the button on the right of the spin buttons. It will open a window where normals can be given in different coordinate systems. Check that in our case a [010] vector chosen in the box basis set makes a plane orthogonal to the y box axis.
• Planes can be rendered or not using the first checkbox in the plane description. Planes can also mask atoms using the second and the third checkbox. Use them and see what happen.
• Planes can be animated to progressively hide or unmask atoms. To do this, click on the "Advanced tools" tab of the "Planes" panel. Select the distance from and to, e.g. From -5 to 5 with a 0.25 step. Then click "Play". All capabilities remain available when playing, especially the masking property or the camera rotation in the rendering window.

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.

• To visualise the cubic directions, we can ask V_Sim to draw the bindings between Si-Si that have the correct length (namely 5.43). To do this, open the "Pairs" window and add a new Si-Si binding with the "+" button. Set the distances to range from (5.4 to 5.45 and choose a different colour from the earlier bindings. New rendered pairs show then the cubic X, Y and Z directions.
• Choose an atom as reference (shift-right-click, e.g. on node 38) and choose three neighbours that will be on X, Y and Z cubic axis (e.g. on node 115, 112 and 106). Drawn distances can be removed in the "Mouse actions" window, using the "Clear" button. In that window, the pick action is also available, selecting the associated radio button. The nodes ids can also be drawn here, selecting the radio button "Draw data on nodes: all". To highlight nodes, use Control left-button.
• Come back to the plane panel and create six planes with the right normals and masking properties to isolate a cubic cell. It may be convenient to hide the FCC box, unchecking the geniuine box in the box tab.
• One can also export or import a list of planes, in the the "Planes" panel, choose the "File tools" tab load for instance this solution file.

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).