Generating crystal models

The Crystal Creator SAMSON App contains the basic tools to write and manipulate crystals. I will show you here how to use it.

Read a crystal structure

To have your first crystal, you can import one. With the Crystal Creator App, you can now read CIF (Crystallographic Information File). First, go fetch some nice crystals on those 2 websites :

I personally advise you to test Macdonaldite, Quartz and Zorite, but please if you have a favourite crystal and you find it, test it.

Open in SAMSON your ‘.cif’ file. A window let you choose the number of crystal unit cells, if you prefer import the mere datas without the symmetries, and  if you want to see the mesh. Click on ‘open’ and the structural model of the crystal and its property model appears in the data graph.

 

Depending on the crystal you have just read, the unit cells of your crystal can be different. Indeed, interesting properties of a crystal appears with randomly distributed defects or substitutions, those are described in the CIF file and are used by the App to create a crystal with proper defects and substitutions.

 

Manipulate a crystal

Right-click on the property model and select “properties”.

The first tabulation of this property window has 4 tools :

  • A button to find back your crystal.
  • A check-box to see its mesh.
  • A tool box to cut your crystal. The 3 first boxes describe the cutting direction (the Miller indexes) and the 4th one the distance, from the position 0, where the cut is done.
  • A tool box to generate another crystal.

The second tabulation is a tool to check if the generated crystal contains the proper amount of defects and substitutions. By clicking on “check atoms ratio”, you can see, for each atom site, if its ratio of presence/absence is respected.

 

Download and open a diamond crystal file and cut it in the direction [111] to see its compact hexagonal structure.

 

Write your own crystal

Click on the Crystal Creator App — the white snow flake — .  In this window, you can :

  • Choose the position 0 of your crystal.
  • Choose the unit cell shape. Either by writing its cell parameters (first tabulation) or directly by writing the unit cell vectors (second tabulation). The button “Write Matrix” and “Write Vectors” allows you to pass from one notation to the other.
  • Choose the atoms composing your unit cell. It should be written like this :
<atom1 symbol> <atom1 x-coordinate> <atom1 y-coordinate> <atom1 z-coordinate>
<atom2 symbol> <atom2 x-coordinate> <atom2 y-coordinate> <atom2 z-coordinate>
<atom3 symbol> <atom3 x-coordinate> <atom3 y-coordinate> <atom3 z-coordinate>
...

The atom symbol has to start by its atomic element symbol (C, Al, Kr …) that can be followed –without space– by other characters to identify it. Depending the tabulation you are in, the atom coordinates are in ‘relative position’, ie a proportion of the unit cell vectors X, Y and Z, or in ‘absolute position’, in angstrom.

  • Choose the number of unit cell you want to generate.

You can also save and load all your crystals by saving their settings (‘save’ icon on the property window).

 

Examples :

For a Face-Centered Cubic (FCC) Aluminum crystal, take a cubic unit cell of lattice parameter 4.05 A, and write in the ‘relative position’ tabulation :

Al 0 0 0 
Al 0 0.5 0.5 
Al 0.5 0 0.5 
Al 0.5 0.5 0

If you want a diamond crystal, you can write choose a cubic unit cell of lattice parameter 3.60 A and write in the ‘relative position’ tabulation :

C0 0 0 0
C1 0.25 0.25 0.25
C2 0 0.5 0.5
C3 0.5 0 0.5
C4 0.5 0.5 0
C5 0.25 0.75 0.75
C6 0.75 0.25 0.75
C7 0.75 0.75 0.25

 

Now, try to create your own Sphalerite (SiZ) crystal, and use the SAMSON tool to create all the bonds.

 

 

Defects in diamond

We will see the effect of defects on the structure of diamond :

  • Load your diamond crystal (the .cif one) and create the bonds.
  • Minimize its structure with the Brenner interaction model.
  • Make a copy of the diamond file and open it in a text editor.
  • At the end of the new file, instead of
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
C 0.00000 0.00000 0.00000

copy and paste :

loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
C 0.00000 0.00000 0.00000 0.95

The inserted line and the last figure means our atom carbon have a probability of 0.95 to be present.

  • Load your diamond with defects, create the bonds.
  • See how the structure changed with defects.

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