Boxes, Crystals, and Grids -

Loading in Crystal Structure Files#

Place .cif and .cssr crystal structure files in PorousMaterials.PATH_TO_CRYSTALS. PorousMaterials.jl currently takes crystals in P1 symmetry only. From here you can start julia and do the following to load a framework and start working with it.

using PorousMaterials

f = Framework("SBMOF-1.cif")

PorousMaterials will then output information about the framework you just loaded:

Name: SBMOF-1.cif
Bravais unit cell of a crystal.
        Unit cell angles α = 90.000000 deg. β = 100.897000 deg. γ = 90.000000 deg.
        Unit cell dimensions a = 11.619300 Å. b = 5.566700 Å, c = 22.931200 Å
        Volume of unit cell: 1456.472102 Å³

Number of atoms = 120
Number of charges = 0
Chemical formula: Dict(:H=>8,:S=>1,:Ca=>1,:O=>6,:C=>14)

Building Blocks of PorousMaterials: Bravais lattice#

We later apply periodic boundary conditions to mimic a crystal of infinite extent. A Box describes a Bravais lattice.

To make a 10 by 10 by 10 Å Bravais lattice with right angles:

box = Box(10.0, 10.0, 10.0, π/2, π/2, π/2)

box.a, box.b, box.c # unit cell dimensions (10.0 Å)
box.α, box.β, box.γ # unit cell angles (1.57... radians)
box.Ω # volume (1000.0 Å³)
box.f_to_c # fractional to Cartesian coordinate transformation matrix
box.c_to_f # Cartesian to fractional coordinate transformation matrix
box.reciprocal_lattice # rows are reciprocal lattice vectors

Replicate a box as follows:

box = replicate(box, (2, 2, 2)) # new box replicated 2 by 2 by 2
box.a # 20 Å

Building Blocks of PorousMaterials: Porous Crystals#

using PorousMaterials

# read in xtal structure file
framework = Framework("SBMOF-1.cif")

# access unit cell box
framework.box

# access Lennard-Jones spheres and point charges comprising the crystal
framework.atoms
framework.charges

# remove annoying numbers on the atom labels
strip_numbers_from_atom_labels!(framework)

# compute crystal density
ρ = crystal_density(framework) # kg/m3

# compute the chemical formula
cf = chemical_formula(framework)

# assign charges according to atom type
charges = Dict(:Ca => 3.0, :O => 2.0, :C => -1.0, :S => 7.0, :H => -1.0)
charged_framework = assign_charges(framework, charges)

# replicate & visualize
framework = replicate(framework, (3, 3, 3))
write_to_xyz(framework, "SBMOF-1.xyz")

Demo of Potential Energy Grid#

Superimpose a grid of points about the unit cell of SBMOF-1. Compute the potential energy of xenon at each point and store as a grid.

using PorousMaterials

framework = Framework("SBMOF-1.cif")
molecule = Molecule("Xe")
forcefield = LJForceField("UFF.csv")

grid = energy_grid(framework, molecule, forcefield,
    n_pts=(50, 50, 50), units=:kJ_mol) # Grid data structure

Write to a .cube volume file to visualize the potential energy contours.

write_cube(grid, "CH4_in_SBMOF1.cube")

Boxes#

# PorousMaterials.Box — Type.

box = Box(a, b, c, α, β, γ, volume, f_to_c, c_to_f, reciprocal_lattice)
box = Box(a, b, c, α, β, γ)
box = Box(f_to_c)

Data structure to describe a unit cell box (Bravais lattice) and convert between fractional and Cartesian coordinates.

Attributes

a,b,c::Float64: unit cell dimensions (units: Angstroms)
α,β,γ::Float64: unit cell angles (units: radians)
Ω::Float64: volume of the unit cell (units: cubic Angtroms)
f_to_c::Array{Float64,2}: the 3x3 transformation matrix used to map fractional

coordinates to cartesian coordinates. The columns of this matrix define the unit cell axes. Columns are the vectors defining the unit cell box. units: Angstrom

c_to_f::Array{Float64,2}: the 3x3 transformation matrix used to map Cartesian

coordinates to fractional coordinates. units: inverse Angstrom

reciprocal_lattice::Array{Float64, 2}: the rows are the reciprocal lattice vectors.

This choice was made (instead of columns) for speed of Ewald Sums.

Loading in Crystal Structure Files#

Building Blocks of PorousMaterials: Bravais lattice#

Building Blocks of PorousMaterials: Porous Crystals#

Demo of Potential Energy Grid#

Boxes#

Crystals#

Grids#