Calcite (CaCO3 )
16. tetr generates a xyz file called geom.xyz. Preview the geometry with any graphical program. Here, we use XMakemol.
CO3
CO3
Ca
Ca
17. From the section ‘‘General settings’’ of the menu we can save the structure by typing S. Then press 8 to save as a VASP (POSCAR) file.
tetr gives you also an option to save the geometry in Cartesian or fractional coordinates (see below) for the POSCAR file. WE save in Cartesian coordinates using C.
18. In “visualization settings” (see below) you can extend the structure periodically with Bb. This will not enlarge your cell, this is only done for visualisation. For example, we extend two-fold along the three lattice vectors by typing 0 1 , 0 1 and 0 1.
19. With XMakemol you just need to press File -> “Revert” to reopen the enlarged structure
[1] and [2] : Enlarged view of calcite from two different prospectives.
[1]
[2]
Note 3: As noted above, the Bb command is just for visualization purposes. This means that tetr will not modify the POSCAR file increasing the number of atoms and extending the lattice vectors. However, since this actual enlargement of the cell might be necessary for some calculations, we show next how to manipulate the primitive cell and save it with tetr.
If you now preview the POSCAR file in a separate X-window, e.g. more POSCAR, you will see this:
