RobertoMD

RobertoMD.jl (JuliaCon2021): Rome-Berlin-Tokyo Hybrid Particle-field Molecular-Dynamics Simulation

A massively parallel hybrid particle-field molecular dynamics simulation package written in Julia. It is aimed to become a productive hPF-MD simulator. However, it has not yet been at that stage. Benchmarks and tests are welcome.

The implemeted functions are limited for now, including:

• Original hPF-MD algorithm of Milano et al..
  • Particle-in-cell transformation
  • Periodic cubic fields (simulation box must be same in x,y,z directions)
• Bond interactions: Harmonic
• Thermostats: Langevin, Berendsen
• Velocity Verlet integration
• Periodic boundary conditions in a cubic box.
• Particle-decomposition parallelization (MPI.jl)

Installation

Julia is required, with Julia v1.5 required to get the latest version of RobertoMD. Install Roberto from the Julia REPL. Enter the package mode by pressing ] and run "add RobertoMD".

Parallelization

The parallelization is implemented via the "particle decomposition" algorithm, taking advantage of the unqiue feature of the field interaction. Details can be found in the previous article [Ref.2].

In short, the field is a function of the local particle density. This collective variable is a slow variable compared to the displacement of the particles. Therefore, it is possible to update the field every $\Delta t$ steps without losing accuracy. In this way, data exchange between different cores is less frequent compared with domain decomposition.

Usage

Several example systems, e.g., monoliquid, polymer melt, copolymer melt, polymer in solution, can be found in Example folder:

This is the hPF-MD simulation of a simple block copolymer system:

using RobertoMD
using Rotations
using JSON

#control parameters
control=Dict(
    "dt"=>0.01,
    "steps"=>1000,
    "velocity verlet"=>true,
    "LAMMPSTrj"=>Dict("file"=>"copolymer.lammpstrj","freq"=>1000),
    "restart"=>Dict("JSONRestart"=>true,"file"=>"copolymer.json","freq"=>1000),
    "BerendsenNVT"=>Dict("tau"=>1.0),
    "harmonic bond"=>Dict(
    "k"=>Dict("1"=>1000.0),
    "l0"=>Dict("1"=>1.0)
    ),
    "Canonical field"=>Dict(
    "χ"=>Dict(  "1"=>[0.0,5.0],
                "2"=>[5.0,0.0] ),
    "κ"=>0.2,
    "uniform mesh"=>true,
    "update"=>1,
    "Lcell"=>1.0),
    "thermo information"=>Dict( "freq"=>1,
                                "energy"=>true,
                                "momentum"=>true,
                                "write"=>true,
                                "file"=>"copolymer.log"),
    "density"=>0.85,
    "bondlength"=>1.0,
    "chain_length"=>20,
    "num_polymers"=>500,
    "zero velocity"=>true,
    )


boxsize=(control["num_polymers"]*control["chain_length"]/control["density"])^(1.0/3)
bondlength=control["bondlength"]
chain_length=control["chain_length"]

polymer=Dict()
for polymer_i in 1:control["num_polymers"]
    polymer[string(polymer_i)]=Dict()
    polymer[string(polymer_i)]["atoms"]=Dict()
    polymer[string(polymer_i)]["bonds"]=Dict()
    pos_init=rand(3)*boxsize
    for monomer_i in 1:chain_length
        r = rand(RotMatrix{3})
        q = QuatRotation(r)
        pos_init=pos_init+q*[bondlength,0.0,0.0]
        type_=1
        if monomer_i>div(control["chain_length"],2)
            type_=2
        end
        polymer[string(polymer_i)]["atoms"][string(monomer_i)]=Dict("type"=>type_,"mass"=>1,"coords"=>pos_init)
    end
    for bond_i in 1:chain_length-1
        polymer[string(polymer_i)]["bonds"][string(bond_i)]=[1,bond_i,bond_i+1]
    end

end

configs=Dict(
    "box"=>[boxsize,boxsize,boxsize],
    "molecules"=>polymer
    )



Simulate(control,configs)

References:

1. Milano, G.; Kawakatsu, T. Hybrid Particle-Field Molecular Dynamics Simulations for Dense Polymer Systems. J. Chem. Phys. 2009, 130 (21), 214106.
2. Zhao, Y.; Nicola, A. D.; Kawakatsu, T.; Milano, G. Hybrid Particle-Field Molecular Dynamics Simulations: Parallelization and Benchmarks. J. Comput. Chem. 2012, 33 (8), 868–880.
3. Bore, S. L.; Cascella, M. Hamiltonian and Alias-Free Hybrid Particle–Field Molecular Dynamics. J. Chem. Phys. 2020, 153 (9), 094106.
4. Wu, Z.; Kalogirou, A.; De Nicola, A.; Milano, G.; Müller‐Plathe, F. Atomistic Hybrid Particle‐field Molecular Dynamics Combined with: Restoring Entangled Dynamics to Simulations of Polymer Melts. J. Comput. Chem. 2021, 42 (1), 6–18.
5. Wu, Z.; Milano, G.; Müller-Plathe, F. Combination of Hybrid Particle-Field Molecular Dynamics and Slip-Springs for the Efficient Simulation of Coarse-Grained Polymer Models: Static and Dynamic Properties of Polystyrene Melts. J. Chem. Theory Comput. 2021 17 (1), 474-487