Configurations

module Configurations

This module defines types and functions for working with atomic configurations of N atoms.

Exported types

• Config

Exported functions

• distance2
• get_distance2_mat

Config(pos::Vector{SVector{3,T}}, bc::BC) where BC <: AbstractBC
Config{N}(pos::Vector{SVector{3,T}}, bc::BC) where BC <: AbstractBC
Config(pos::PositionArray, bc::BC) where BC <: AbstractBC

Generates a configuration of N atomic positions, each position saved as SVector of length 3.

• Fieldnames:
  • pos: vector of x,y, and z coordinates of every atom
  • bc: boundary condition

distance2(a::PositionVector,b::PositionVector) 
distance2(a::PositionVector,b::PositionVector,bc::SphericalBC)
distance2(a::PositionVector,b::PositionVector,bc::CubicBC)
distance2(a::PositionVector,b::PositionVector,bc::RhombicBC)

Method 1&2 - Finds the distance between two positions a and b. Method 3 - Finds the distance between two positions a and the nearest image of b in a cubic box. Method 4 - Finds the distance between two positions a and the nearest image of b in a rhombic box. Minimum image convension in the z-direction is the same as the cubic box. In x and y-direction, first the box is transformed into a rectangular box, then MIC is done, finally the new coordinates are transformed back.

get_centre(position::PositionArray,N::Int64)

Function to find the centre of mass of a configuration. Accepts the positions and number of positions and calculates the xyz coordinates of their centre.

get_distance2_mat(conf::Config{N})

Builds the matrix of squared distances between positions of configuration.

get_tan(a::PositionVector,b::PositionVector)
get_tan(a::PositionVector,b::PositionVector,bc::SphericalBC)
get_tan(a::PositionVector,b::PositionVector,bc::CubicBC)
get_tan(a::PositionVector,b::PositionVector,bc::RhombicBC)

Method 1&2 : tan of the angle between the line connecting two points a and b, and the z-direction Method 3: tan of the angle between the line connecting two points a and the nearest image of b, and the z-direction in a cubic boundary Method 4: tan of the angle between the line connecting two points a and the nearest image of b, and the z-direction in a rhombic boundary

get_tantheta_mat(conf::Config,bc::BC) where BC <: AbstractBC

Builds the matrix of tan of angles between positions of configuration in a spherical boundary.

get_volume(bc::CubicBC)
get_volume(bc::RhombicBC)

Returns the volume of a box according to its geometry for use where the ensemble does not imply a fixed V.

recentre!(conf::Config{N,BC,T}) where {N,BC,T}

Function to change the centre of mass of a configuration conf to [0,0,0] in Cartesian space.