More generic propagator

[Luthaf]

It would be great to have a Propagator type, with the following subtypes :

• MolecularDynamic
• Replay (the current interface for read/write the trajectories)
• Minimisation with it's own subtypes :
  • Gradient descent ;
  • Any other useful minimisation algorithm

[Luthaf]

More thought about this point: we can define the Simulation type as follow

type Simulation{T<:Propagator}
    propagator::Propagator
    interactions :: Interactions
    controls :: Vector{BaseControl}
    checks :: Vector{BaseCheck}
    computes :: Vector{BaseCompute}
    outputs :: Vector{BaseOutput}
# Data
    topology :: Topology
    cell :: UnitCell
    frame :: Frame
    masses :: Vector{Float64}
# all other data to be shared
    data :: Dict{Symbol, Any}
end

And then have

type MolecularDynamic <: Propagator
    forces_computer :: BaseForcesComputer
    integrator :: BaseIntegrator
    forces :: Array3D{Float64}
end

type Metadynamic <: Propagator
    md :: MolecularDynamic
    gaussians::Array{Float64, 1}
    # other parameters
end

type Replay <: Propagator
    reader :: Reader
end

type MonteCarlo <: Propagator
    moves::Array{Move, 1}
    energy_computer::energy
end

# And so on

[Luthaf]

Done in 1e696ac28154640d4432b7ebd64f099ec1a16b23