FastSpecSoG.jl is an implementation of the newly developed fast spectral sum-of-Gaussian method for the calculation of the electrostatic potential and field in double periodic molecular systems in Julia Programming Language.
The method is based on the sum-of-Gaussian (SoG) approximation, the Non-Uniform Fast Fourier Transform (NUFFT) algorithm and the FFT-FFCT mixed algorithm and reached a complexity of
For more details about our method, please refer to our arxiv article A fast spectral sum-of-Gaussians method for electrostatic summation in quasi-2D systems. For benchmarks, please see this repo https://github.com/ArrogantGao/FSSoG_benchmark.
First you need to add its deps ExTinyMD in Julia by typing ] in Julia REPL and then
pkg> add ExTinyMDThen you can add this package by typing
pkg> add FastSpecSoGto install the package.
In this package, two sets of method are implemented. Consider a simulation box with edge length
For cubic systems, please refer to the following example:
n_atoms = 100
L = 50.0
boundary = ExTinyMD.Q2dBoundary(L, L, L)
atoms = Vector{Atom{Float64}}()
for i in 1:n_atoms÷2
push!(atoms, Atom(type = 1, mass = 1.0, charge = 2.0))
end
for i in n_atoms÷2 + 1 : n_atoms
push!(atoms, Atom(type = 2, mass = 1.0, charge = - 2.0))
end
info = SimulationInfo(n_atoms, atoms, (0.0, L, 0.0, L, 0.0, L), boundary; min_r = 1.0, temp = 1.0)
r_c = 10.0
N_real = (128, 128, 128)
w = (16, 16, 16)
β = 5.0 .* w
extra_pad_ratio = 2
cheb_order = 10
preset = 3
M_mid = 3
N_grid = (32, 32, 32)
Q = 48
R_z0 = 32
Q_0 = 32
fssog_interaction = FSSoGInteraction((L, L, L), n_atoms, r_c, Q, 0.5, N_real, w, β, extra_pad_ratio, cheb_order, M_mid, N_grid, Q, R_z0, Q_0; preset = preset, ϵ = 1.0)
fssog_neighbor = CellList3D(info, fssog_interaction.r_c, fssog_interaction.boundary, 1)
energy_sog = ExTinyMD.energy(fssog_interaction, fssog_neighbor, info, atoms)For slab systems, please refer to the following example
n_atoms = 100
Lx = 100.0
Ly = 100.0
Lz = 1.0
boundary = ExTinyMD.Q2dBoundary(Lx, Ly, Lz)
atoms = Vector{Atom{Float64}}()
for i in 1:n_atoms÷2
push!(atoms, Atom(type = 1, mass = 1.0, charge = 2.0))
end
for i in n_atoms÷2 + 1 : n_atoms
push!(atoms, Atom(type = 2, mass = 1.0, charge = - 2.0))
end
info = SimulationInfo(n_atoms, atoms, (0.0, Lx, 0.0, Ly, 0.0, Lz), boundary; min_r = 1.0, temp = 1.0)
r_c = 1.0
N_real = (128, 128)
R_z = 32
w = (16, 16)
β = 5.0 .* w
cheb_order = 16
preset = 3
Q = 48
Q_0 = 32
R_z0 = 32
Taylor_Q = 24
fssog_interaction = FSSoGThinInteraction((Lx, Ly, Lz), n_atoms, r_c, Q, 0.5, N_real, R_z, w, β, cheb_order, Taylor_Q, R_z0, Q_0; preset = preset, ϵ = 1.0)
fssog_neighbor = CellList3D(info, fssog_interaction.r_c, fssog_interaction.boundary, 1)
energy_sog = ExTinyMD.energy(fssog_interaction, fssog_neighbor, info, atoms)If you use this package in your research, please cite our article:
@article{fssog,
title={{A fast spectral sum-of-Gaussians method for electrostatic summation in quasi-2D systems}},
author={Xuanzhao Gao and Shidong Jiang and Jiuyang Liang and Zhenli Xu and Qi Zhou},
year={2024},
journal={arXiv preprint arXiv:2412.04595},
}