CASTEP Visualisation using gdis

Another useful viewer is gdis. Although its rendering of isosurfaces is so poor that I do not describe it here, it does handle crystals better than Jmol, and, unlike Jmol or XCrysDen, allows one to edit structures (move or delete atoms) trivially. Unlike the other examples, this one was run under Linux, not Tru64. For various reasons gdis is considerably more stable on Linux.

As an example, we start with a simple 8-atom cubic silicon unit cell.

8 atom Si cell

Then, we click on the "model periodic image" box, and show two unit cells in all three directions.

64 atom Si cell

By choosing Tools, Model editing, Periodicity, Make supercell, we can make this 64 atom cell the new unit cell. A left click on an atom highlights that atom. One can now change the co-ordinates of the selected atom by typing into the co-ordinate display at the left, delete it by selecting Edit, Delete, or change its type by changing its label to another atomic symbol. Here it has been changed to phosphorous, and displaced slightly from the symmetric site.

64 atom Si cell with phosphorous

Then one can save the new structure as a pdb file, using File, Save as, and an .pdb extension, and then convert the co-ordinates back to a CASTEP .cell file with

check2xsf --cell si63p.pdb si63p.cell

Note that the resulting .cell file contains only atomic positions and the unit cell axes. Worrying about symmetry, k-points and pseudopotentials is now your job.

To remove the black background (e.g. for printing) select View, Display Properties, Colours. Note that gdis sometimes fails to calculate bonds correctly. One can add them by hand: Tools, Model Editing, Single Bonds, and then click on the two atoms needing a bond.

Back to CASTEP visualisation using free software overview.