LightLattices.jl

The package provides a convenient interface to work with Lattices with arbitrary reapeated basis cells.

For the exported types of basis cells and lattices, it defines the array interface which allows to access the coordinate of specific node by its index. In addition to that, it provides a function relative_coordinate which allows to calculate the shortest vector connecting the two nodes.

Overview

The package exports the type RegularLattice{D,T} and several types used to describe the basis cell of the lattice. All the exported types are subtypes of the abstract type AbstractNodeCollection{D,T}. Here, D refers to the dimensionality of space (number of coordinates), T refers to the type used to store the coordinates. For all the exported subtypes, the package defines the array interface

node_collection[I]

which allows to access the coordinate of the I-th node of the collection. In addition to that, the package provides the function relative_coordinate:

relative_coordinate(node_collection::AbstractNodeCollection, I1, I2)

which returns the vector connecting the I2-th node with the I1-th node. In the case of RegularLattice-s with periodic boundary conditions, relative_coordinate returns the shortest connecting vector. (Actually, in the case of complex basis cell, there can be several "shortest" vectors. The problem is resolved by a simple heuristic, described in the docs).

There are three available types to describe the basis cell: HomogeneousCell, TrivialCell and InhomogeneousCell. HomogeneousCell refers to a homogeneous collection of nodes. TrivialCell behaves like HomogeneousCell with single node at the origin (zero coordinates). Finally, InhomogeneousCell is useful in the situation where one need to distinguish between several groups of nodes in the basis cell. For example, we can have several groupes of nodes corresponding to the different types of nuclei which occupy these nodes.

For the detailed account of exported types and the interface, please look at the manual section of the docs.

Examples

Chain

Here we construct a periodic chain with 11 nodes. The separation between nodes is 1 by default.

using LightLattices

chain = RegularLattice((11,); label=:chain)

Square Lattice

Now, let us construct a square 11x11 lattice with the size of the square equal to 2.

using LightLattices

square_lattice = RegularLattice((11,11), 2; label = :square)

Cubic Lattice

For the cubic lattice example, let us draw inspiration from the real world. The Fluorine nuclei in CaF2 consitute a cubic lattice with lattice parameter a=2.725 Å. Let us construct fluorine sublattice of size 11x11x11 with free boundary conditions:

using LightLattices, Unitful

fluorine_sublattice = RegularLattice((11,11,11), 2.725u"Å"; label=:cubic, periodic=false)

Diamond lattice with homogeneous basis cell.

The lattice of diamond is face-centered cubic with a basis cell consisting of two nodes. Let us take the size of cube equal to 1. The following creates diamond lattice with 11x11x11 basis cells with periodic boundary conditions:

using LightLattices

fcc_pvecs = 0.5*hcat([0,1,1],[1,1,0],[1,0,1]) |> SMatrix{3,3}

diamond_cell = HomogeneousCell([[0.0,0.0,0.0], [0.25,0.25,0.25]]; label = :diamond)
dimond_lattice = RegularLattice((11,11,11), fcc_pvecs, diamond_cell; label=:fcc)

Here, HomogeneousCell constructor takes the vector of coordinates of the nodes. Coordinates can be expressed as Vector-s, SVector-s or NTuple-s. Under the hood, all coordinates are converted to SVector-s.

Magnetic sublattice of fluorapatite with inhomogeneous basis cell.

This example is going to be quite elaborated, but it illustrates the application of additional type of basis cell: InhomogeneousCell. Fluorapatite has the hexagonal structure with the space group P6_3/m. The three lattice parameters are a=b=9.462 Å and c=6.849 Å. The c-axis is orthogonal to (a, b) plane and the angle between a and b is 120°. Thus, we can construct the matrix of primitive vectors as

using Unitful

const a = 9.462u"Å"
const c = 6.849u"Å"

fpvecs = hcat(a*[0.5, 0.5*sqrt(3), 0.0],
              a*[0.5, -0.5*sqrt(3), 0.0],
              c*[0.0, 0.0, 1.0]
             ) |> SMatrix{3,3}

The basis cell for magnetically active sublattice of fluorapatite contains two F nuceli at positions

$$[0.0,0.0,0.25], [0.0,0.0,0.75]$$

and six P nuclei at positions

$$[x,y,0.25], [1-y,x-y,0.25], [y-x,1-x,0.25], [1-x,1-y,0.75], [y, y-x,0.75], [x-y, x, 0.75],$$

where x=0.369 and y=0.3985. All the coordinates here are relative to the set of primitive vectors fpvecs.

Since we have two different types of nuclei, it is a good idea somehow to separate two groups of nuclei in the basis cell. In this case, one should use InhomogeneousCell.

const x = 0.369
const y = 0.3985

cell_vectors_raw1 = [[0.0, 0.0, 0.25], [0.0, 0.0, 0.75]]
cell_vectors_raw2 = [[x, y, 0.25], [-y, x-y, 0.25], [y-x, -x, 0.25],
                  [-x, -y, 0.75], [y, y-x, 0.75], [x-y, x, 0.75]]

fcell = InhomogeneousCell([fpvecs*vec for vec in cell_vectors_raw1], [fpvecs*vec for vec in cell_vectors_raw2]; label = :fluorapatite_magnetic)

Finally, we can construct the lattice. Let us choose the size of 11x11x11 basis cells and periodic boundary conditions.

fluorapatite_magnetic_sublattice = RegularLattice((11,11,11), fpvecs, fcell; label = :hexagonal)