Matter is the foundation for every data type defined in PorousMaterials. Two structs are used to define all atomic structures: Atoms and Charges. Every atom, molecule, or crystal structure can be simulated by understanding its atoms and its point charges.

We chose to store each collection as a single object (Atoms) rather than an array of objects (Array{Atom}) because it allows us to store the locations in contiguous memory. We found significant speed increases when storing each collection as a single object.

One array of locations also allowed us to take advantage of broadcasting. For example, it is useful when calculating the energy inside a framework. Instead of looping through every atom, we can instead run this line:

dxf = broadcast(-, framework.atoms.xf, molecule.atoms.xf[i])

This calculates the distance between one atom in a molecule and every atom in the framework.

Building Blocks of PorousMaterials: Matter#

In PorousMaterials.jl, crystals and molecules are composed of Atoms and Charges

To create a carbon atom at [0.1, 0.2, 0.5] fractional coordinates (in the context of some Bravais lattice):

xf = Array{Float64, 2}(undef, 3, 0)
xf = [xf [0.1, 0.2, 0.5]]
atoms = Atoms([:C], xf) # constructor
atoms.species[1] # :C
atoms.xf[:, 1] # [0.1, 0.2, 0.5]

To create a point charge of +1 at [0.1, 0.2, 0.5] fractional coordinates (in the context of some Bravais lattice):

xf = Array{Float64, 2}(undef, 3, 0)
xf = [xf [0.1, 0.2, 0.5]]
charges = Charges([1.0], xf)
charges.q[1] # 1.0
charges.xf[:, 1] # [0.1, 0.2, 0.5]

Matter#

# PorousMaterials.Atoms — Type.

Data structure holds a set of atom species and their positions in fractional coordinates.

Fractional coords of atom i is charges.xf[:, i].

Example use

atoms = Atoms(2, [:C, :F], [0.0 1.0; 2.0 3.0; 4.0 5.0])

Attributes

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# PorousMaterials.Charges — Type.

Data structure holds a set of point charges and their positions in fractional coordinates.

Fractional coords of charge i is charges.xf[:, i].

Example use

charges = Charges(2, [-1.0, 1.0], [0.0 1.0; 2.0 3.0; 4.0 5.0])

Attributes

source