Example structure: SBMOF-1.
Goal of visualization:
The unit cell box is described by unitcellboundary.vtk
The atom types and their Cartesian coordinates are described in SBMOF1.xyz.
To read these into Julia, I wrote reader.jl:
include("reader.jl")
i = 1 # first atom
atoms[i] # gives element type
x[:, i] # gives Cartesian coordinate of element i
atom_colors[i] # gives color atom i should be in visualization (RGB tupble)
atom_radii[i] # gives radius of atom i (usually these are scaled in visualization)
Should the user specify the bonding rules, i.e. a list of which atoms are bonded? What is a good format? Just a list of edges? e.g.
bonds.txt
1 2 # atom 1 is bonded with atom 2
4 9 # atom 4 is bonded with atom 9
?
One typically needs to tune the bonding rules in a visualization. Default bonding rules are:
Let X be any atom. Let Y be any other atom.
If atom Y is hydrogen H: if distance between Y and X is less than 1.2, create a bond.
If atom Y is any other atom type: if distnace between X and Y is less than 1.9, create a bond.