Algorithms for all simulations

Computing values

Algorithms to compute properties from a simulation are called Compute in Jumos. They all act by taking an Universe as parameter, and then setting a value in the dictionary.

To add a new compute algorithm (we will call it MyCompute), we have to subtype Jumos.Simulations.BaseCompute and provide specialised implementation for the function; with the following signature:, ::Universe)

This function can set a entry with a Symbol key to store the computed value. This value can be anything, but basic types (scalars, arrays, etc.) are to be prefered.

Outputing values

An other way to create a custom output is to subtype Output. The subtyped type must have at least one field: frequency::OutputFrequency, which is responsible for selecting the write frequency of this output. Two functions can be overloaded to set the output behaviour.

Base.write(::Output, context::Dict{Symbol, Any})

Write the ouptut. This function will be called every n simulation steps according to the frequency field.

The context parameter contains all the values set up by the computation algorithms, and a special key :frame refering to the current simulation frame.

Jumos.setup(::Output, ::Simulation)

This function is called once, at the begining of a simulation run. It should do some setup job, like adding the needed computations algorithms to the simulation.

As an example, let’s build a custom output writing the x position of the first atom of the simulation at each step. This position will be taken from the frame, so no specific computation algorithm is needed here. But this position will be writen in bohr, so some conversion from Angstroms will be needed.

# File FirstX.jl

using Jumos

import Base.write
import Jumos.setup

type FirstX <: Output

# Default values constructor
function FirstX(filename, frequency=1)
    file = open(filename, "w")
    return FirstX(file, OutputFrequency(frequency))

function write(out::FirstX, context::Dict)
    frame = context[:frame]
    x = frame.positions[1][1]
    x = x/0.529 # Converting to bohr
    write(out.file, "$x \n")

# Not needed here
# function setup(::FirstX, ::Simulation)

This type can be used like this:

using Jumos

sim = Simulation(:md, 1.0)
# ...

push!(sim, FirstX("The-first-x-file.dat"))