8. TheorChem2Blender - Unit cells, growth, Miller planes, and polyhedra

Overview

TheorChem2Blender is a program that has 6 tabs: Input, Customization, Ions, Unit Cells, Output, and Convert!. Which tabs to modify depend on the type of 3D file the user wants to create. The Unit Cells tab is different from the others covered so far - it only becomes available when the input file type is .vasp, since periodic cell information is read from VASP-format files. Below is a continuation on how to use TheorChem2Blender, focused on rendering unit cell boundaries, growing supercells, drawing crystallographic (Miller) planes, and building coordination polyhedra from a .vasp input. Refer to (3) basic use for the general input/convert workflow.

Input tab

  1. Change the input type to .vasp

  2. Click on set to select the input name

  3. Go to input_examples/vasp_files/

  4. Select SrTiO3_perovskite.vasp as the input

  5. Notice the Unit Cells tab, previously greyed out, is now available - this only happens for .vasp input

  6. Go to the Unit Cells tab

Unit Cells tab

  1. If you defined cell boundaries in the .vasp file using a bond order of 0.5, check unit cell boundaries to render them as solid unit cell edges instead of dashed lines

  2. Check allow unit cell growth to render one or more duplicated copies of the unit cell

  3. Click add cell growth, then choose how many times to repeat the cell along x, y, and z - for this example, try 2, 2, 2

x: 2  y: 2  z: 2

  1. Click add cell growth again if you want to render more than one growth size in the same batch - for example, also add 1, 1, 1 to keep the original cell alongside the 2x2x2 supercell

  2. Check allow Miller indices to render crystallographic planes

  3. Click add plane, then choose h, k, and l - for this example, try 1, 0, 0

h: 1  k: 0  l: 0

  1. Click add plane again for more planes, e.g. 1, 1, 1. Every plane you add is rendered on every unit cell growth size defined in steps 9-10

  2. Check build polyhedra to draw coordination polyhedra around selected center atoms

  3. Click add center, then choose the element that will act as the polyhedron center - for this example, choose Ti, so a polyhedron is drawn around every titanium atom with three or more bonded oxygen neighbors

  4. Click add center again to build polyhedra around a second element type, if desired

  5. Click Clear at any point to reset unit cell boundaries, growth, Miller planes, and polyhedra back to empty

  6. Go to the Convert! tab

Convert! tab

  1. Click on Convert!

  2. If you added more than one unit cell growth size, one output file is generated per growth size, each with every Miller plane rendered on it

  3. Your file(s) will appear by default in the output/ folder

Note

🎥 To see a video recording of this walkthrough, visit the following link: [video coming soon]

Previous: (7) animating xyz files

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