The Spatial Box

Within PorousMaterials.jl, the 3D space in which all Coords are located is the Box. Each Crystal has its own Box, equivalent to the unit cell of a material, containing as attributes the unit cell edge lengths (a b c), crystallographic dihedral angles (α β γ), volume, conversion factors for translating between Fractional and Cartesian coordinates, and the reciprocal (Fourier transform) vectors for the Bravais lattice.

defining a box

A Box is most conveniently constructed from its basic spatial data (a b c α β γ). For example, given the unit cell of Co-MOF-74, we can define its Box:

a = 26.13173 # Å
b = 26.13173
c = 6.722028
α = π/2 # radians
β = π/2
γ = 2*π/3
box = Box(a, b, c, α, β, γ)
# output
Bravais unit cell of a crystal.
	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000000 deg.
	Unit cell dimensions a = 26.131730 Å. b = 26.131730 Å, c = 6.722028 Å
	Volume of unit cell: 3975.275878 ų

A Box may also be defined by providing only the Fractional-to-Cartesian conversion matrix:

box = Box([26.1317 -13.0659 0; 0 22.6307 0; 0 0 6.72203])
# output
Bravais unit cell of a crystal.
	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg.
	Unit cell dimensions a = 26.131700 Å. b = 26.131711 Å, c = 6.722030 Å
	Volume of unit cell: 3975.265115 ų

To quickly get a simple unit-cubic Box, use the unit_cube function.

unit_cube()
# output
Bravais unit cell of a crystal.
	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 90.000000 deg.
	Unit cell dimensions a = 1.000000 Å. b = 1.000000 Å, c = 1.000000 Å
	Volume of unit cell: 1.000000 ų

transforming coordinates

Conversions are provided for switching between Fractional and Cartesian Coords using the Box (works for Atoms and Charges, too)

xtal = Crystal("SBMOF-1.cif")
Cart(xtal.atoms.coords, xtal.box)
# output
Cart([4.594867082350715 -0.952720283971488 … 0.8392490029633858 -1.5321086078257065; 1.4395486200000005 4.2228986200000005 … 1.4289162230000012 4.212266223; 5.89964228469024 5.359217037237699 … 17.537474811394276 16.239103154389543])

replicating a box

For simulations in larger volumes than a single crystallograhic unit cell, the Box may be replicated along each or any of the three crystallographic axes.

replicated_box = replicate(box, (2,2,2))
# output
Bravais unit cell of a crystal.
	Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg.
	Unit cell dimensions a = 52.263400 Å. b = 52.263422 Å, c = 13.444060 Å
	Volume of unit cell: 31802.120923 ų

exporting a box

For visualization of the unit cell boundaries, the Box may be written out to a .vtk file for use in Visit

write_vtk(box, "box.vtk")
# output
See box.vtk

detailed docs