ChebParticleMesh.jl

ChebParticleMesh.jl is a package based on Julia, which provide a set of tools for the widely used Particle-Mesh methods. Using the tools provided by this package, you can easily create a uniform grid with arbitrary dims and periodicity, and then interpolate the particles onto the grid with provided/self-defined window functions so that the problem can be transformed into reciprocal space via Fast Fourier Transform and then being solved there.

Getting Started

Add this package in julia by typing ] in Julia REPL and then type

pkg> add ChebParticleMesh

to install the package.

Introduction

In this package, the process of Particle-Mesh is divided into SIX different steps, including

1. Pre-computating: Generating the grid, the window function and scaling factors
2. Interpolation: Interpolating the point sources onto the grids
3. FFT: Using FFT to transform the density on grids into the reciprocal space
4. Scaling: Scale the fourier modes with the Green's function
5. IFFT: Using IFFT to transform the grid back to the real space
6. Gathering: Integrate the potential on the grid back to the particles

Specially, this package is called ChebParticleMesh.jl because we provided tools to approximate the window functions via piecewise Chebyshev poly, so that the calculation can be much faster when using some complicated kernels, such as the KB-kernel. In this package, only pre-computation leads to huge allocation but only needed to be calculated once before the calculation. FFT and IFFT needs 4 allocations by FFTW; interpolating, scaling and gathering are allocation free, so that the package is highly efficient.

Examples of Use

Implentation of PPPM

In the following example, we will show how to use the ChebParticleMesh.jl to implentate the long-range part of the well known P3M method.

The target is to compute the double summation: $\sum_{\mathbf{m} \in \mathbb{Z}^3} \sum_{i, j} q_i q_j \frac{\mathrm{erf}( \alpha (r_{ij} + L_m))}{r_{ij} + L_m}$. where $\mathrm{erf}(\cdot)$ for the error function and $\mathbf{L_m} = (m_x L_x, m_y L_y, m_z L_z)$ for the periodic images.

First we set up the system:

L = 10.0, 10.0, 10.0 # size of the box
periodicity = (true, true, true) # fully periodic
extra_pad = (0, 0, 0) # no extra padding needed
N_real = (16, 16, 16) # 16 grids in each direction in real space
w = N_real ./ 4 # cutoff of interpolating
α = 0.5

Precomputation:

# Grid generation
gridinfo = GridInfo(N_real, w, periodicity, extra_pad, L)
gridbox = GridBox(gridinfo)

# using the Wkb window function, and generate its Chebyshev approximation
f_window = [x -> Wkb(x, (w[i] + 0.5) * gridinfo.h[i], 5.0 * w[i]) for i in 1:3]
cheb_coefs = tuple([ChebCoef(f_window[i], gridinfo.h[i], w[i], 10) for i in 1:3]...)

# using the Fourier transform of the window function and Green's function in Fourier space to generate the scaling factors
F_f_window = [x -> FWkb(x, (w[i] + 0.5) * gridinfo.h[i], 5.0 * w[i]) for i in 1:3]
func_scale = (kx, ky, kz) -> iszero(kx^2 + ky^2 + kz^2) ? zero(T) : (F_f_window[1](kx) * F_f_window[2](ky) * F_f_window[3](kz))^(-2) * exp(-(kx^2 + ky^2 + kz^2) / (4*α^2)) / (kx^2 + ky^2 + kz^2)
scalefactor = ScalingFactor(func_scale, gridinfo)

Generate some randomly allocated particles as input

n_atoms = 200
qs = 2.0 .* rand(n_atoms) .- 1.0
qs .-= sum(qs) / n_atoms
poses = [L .* (rand(), rand(), rand()) for i in 1:n_atoms]

Compute:

interpolate!(qs, poses, gridinfo, gridbox, cheb_coefs)
fft!(gridbox)
scale!(gridbox, scalefactor)
ifft!(gridbox)
E = gather(qs, poses, gridinfo, gridbox, cheb_coefs) / 8π

The full script is given in example/PPPM.jl, the result is compared with a mesh-free method, Ewald3D provided by EwaldSummations.jl and shows great convergency as the number of grid points increase.

How to Contribute

If you find any bug or have any suggestion, please open an issue.