CellListMap.jl

This package is for computing interactions or any other property dependent on the distances between pairs of two- or three-dimensional particles, within a cutoff. It maps a function to be computed pairwise using cell lists, using periodic boundary conditions of any type. Parallel and serial implementations can be used.

It allows the fast computation of any quantity from the pairs that are within the desired cutoff, for example an average distance or an histogram of distances, forces, potentials, minimum distances, etc., as the examples below illustrate. This is done by passing the function to be evaluated as a parameter of the map_pairwise! function.

Installation

julia> import Pkg

Overview

The main function is map_parwise! (or map_pairwise):

If the analysis is performed on the pairs of a single vector x (n*(n-1)/2 pairs), the function can be called with:

map_pairwise!(f::Function,output,box::Box,cl::CellList)

while if two distinct sets of points are provided (n*m pairs), it is called with:

map_pairwise!(f::Function,output,box::Box,cl::CellListPair)

where the cl variable of type CellList or CellListPair contains the cell lists built from the coordinates of the system, and box contains the system box properties.

These functions will run over every pair of particles which are closer than box.cutoff and compute the (squared) Euclidean distance between the particles, considering the periodic boundary conditions given in the Box structure. If the distance is smaller than the cutoff, a user defined function f of the coordinates of the two particles will be computed.

The function f receives six arguments as input:

f(x,y,i,j,d2,output)

Which are the coordinates of one particle, the coordinates of the second particle, the index of the first particle, the index of the second particle, the squared distance between them, and the output variable. It has also to return the same output variable. Thus, f may or not mutate output, but in either case it must return it. The squared distance d2 is computed internally for comparison with the cutoff, and is passed to the f because many times it is used for the desired computation. Thus, the function f that is passed to map_pairwise! must be always of the form:

function f(x,y,i,j,d2,output)
# update output
return output
end

and the user can define more or less parameters or additional data required to compute the function using closures, as shown in the examples.

Parallel calculations are the default if more than one thread is available. Use parallel=false as an optional argument to map_pairwise! to run the serial version instead.

Mutable and immutable outputs

map_pairwise! and map_pairwise (with the bang, or not) are aliases of the same function, which always returns the result value. It is a convention in Julia that functions ending with the ! mutate the arguments, while those without do not. Here, this behavior is dependent on the type of input. If the output variable is immutable, its value won't be mutated, and the assignment of the result to the output value depends on explicit assignment. In these cases, it is customary to use the map_pairwise (without !) function name:

output = map_pairwise(function, output0, box, cl)

where output0 represents the initial value of the immutable output. When, on the contrary, the output is a mutable variable (an array, for example), the map_pairwise! version is preferred for code clarity, and the reassignment is not needed (nor recommendable):

output = zeros(10) # example of mutable output
map_pairwise!(function, output, box, cl)