UnitCell¶
A simulation cell (UnitCell
type) is the virtual container in which all the
particles of a simulation move. The UnitCell type is parametrized by the
celltype
. There are three different types of simulation cells:
 Infinite cells (
InfiniteCell
) do not have any boundaries. Any move is allowed inside these cells;  Orthorombic cells (
OrthorombicCell
) have up to three independent lenghts; all the angles of the cell are set to 90° (\(\pi/2\) radians)  Triclinic cells (
TriclinicCell
) have 6 independent parameters: 3 lenghts and 3 angles.
Creating simulation cell¶

UnitCell
(A[, B, C, alpha, beta, gamma, celltype])¶ Creates an unit cell. If no
celltype
parameter is given, this function tries to guess the cell type using the following behavior: if all the angles are equals to \(\pi/2\), then the cell is anOrthorombicCell
; else, it is aTriclinicCell
.If no value is given for
alpha, beta, gamma
, they are set to \(\pi/2\). If no value is given forB, C
, they are set to be equal toA
. This creates a cubic cell. If no value is given forA
, a cell with lenghts of 0 Angström and \(\pi/2\) angles is constructed.julia> UnitCell() # Without parameters OrthorombicCell Lenghts: 0.0, 0.0, 0.0 julia> UnitCell(10.) # With one lenght OrthorombicCell Lenghts: 10.0, 10.0, 10.0 julia> UnitCell(10., 12, 15) # With three lenghts OrthorombicCell Lenghts: 10.0, 12.0, 15.0 julia> UnitCell(10, 10, 10, pi/2, pi/3, pi/5) # With lenghts and angles TriclinicCell Lenghts: 10.0, 10.0, 10.0 Angles: 1.5707963267948966, 1.0471975511965976, 0.6283185307179586 julia> UnitCell(InfiniteCell) # With type InfiniteCell julia> UnitCell(10., 12, 15, TriclinicCell) # with lenghts and type TriclinicCell Lenghts: 10.0, 12.0, 15.0 Angles: 1.5707963267948966, 1.5707963267948966, 1.5707963267948966

UnitCell
(u::Vector[, v::Vector, celltype]) If the size matches, this function expands the vectors and returns the corresponding cell.
julia> u = [10, 20, 30] 3element Array{Int64,1}: 10 20 30 julia> UnitCell(u) OrthorombicCell Lenghts: 10.0, 20.0, 30.0
Indexing simulation cell¶
You can access the cell size and angles either directly, or by integer indexing.

getindex
(b::UnitCell, i::Int)¶ Calling
b[i]
will return the corresponding length or angle : fori in [1:3]
, you get thei
^{th} lenght, and fori in [4:6]
, you get [avoid get] the angles.In case of intense use of such indexing, direct field access should be more efficient. The internal fields of a cell are : the three lenghts
a, b, c
, and the three anglesalpha, beta, gamma
.
Boundary conditions and cells¶
Only fully periodic boundary conditions are implemented for now. This means that if a particle crosses the boundary at some step, it will be wrapped up and will appear at the opposite boundary.
Distances and cells¶
The distance between two particles depends on the cell type. In all cases, the minimal image convention is used: the distance between two particles is the minimal distance between all the images of theses particles. This is explicited in the Periodic boundary conditions and distances computations part of this documentation.