update interface

HPMolSim · Dec 17, 2024 · 4cf9d44 · 4cf9d44
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diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "EwaldSummations"
 uuid = "329efeb5-5dc7-45f3-8303-d0bcfeef1c8a"
 authors = ["Xuanzhao Gao <[email protected]>"]
-version = "0.1.3"
+version = "0.2.0"
 
 [deps]
 CellListMap = "69e1c6dd-3888-40e6-b3c8-31ac5f578864"
@@ -24,6 +24,7 @@ julia = "1.10"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [targets]
-test = ["Test"]
+test = ["Test", "Random"]
diff --git a/README.md b/README.md
@@ -43,6 +43,8 @@ Here is an example for calculating energy of 3D systems, via Ewald3D or directio
 
 ```julia
 # Init the system
+using ExTinyMD, EwaldSummations
+
 n_atoms = 100
 L = 100.0
 boundary = Boundary((L, L, L), (1, 1, 1))
@@ -117,8 +119,8 @@ n_atoms = 100
 L = 100.0
 boundary = ExTinyMD.Q2dBoundary(L, L, L)
 
-s = 6.0
-alpha = 2.0
+s = 3.0
+alpha = 0.2
 γ = (0.9, 0.9)
 N_img = 10
 N_pad = 20
@@ -147,8 +149,17 @@ ICMEwald2D_interaction = IcmEwald2DInteraction(n_atoms, s, alpha, γ, (L, L, L),
 energy_icmewald2d = ICM_Ewald2D_energy(ICMEwald2D_interaction, coords, charge)
 
 # ICM-Ewald3D, consider 20 layers of image charges and 40 layers of padding
-ICMEwald3D_interaction = IcmEwald3DInteraction(n_atoms, s, alpha, γ, (L, L, L), N_pad, N_img)
-energy_icmewald3d = ICMEwald3D_energy(ICMEwald3D_interaction, coords, charge)
+ICMEwald3D_interaction = IcmEwald3DInteraction(n_atoms, s, alpha, γ, (L, L, L), N_img, N_pad)
+energy_icmewald3d = ICM_Ewald3D_energy(ICMEwald3D_interaction, coords, charge)
+```
+
+## Citation
+
+If you use this package in your research, please cite at least one of the following paper:
+
+```
+
+
 ```
 
 ## How to Contribute

diff --git a/src/types.jl b/src/types.jl
@@ -8,6 +8,8 @@ struct Ewald2DInteraction{T} <: ExTinyMD.AbstractInteraction
     k_set::Vector{Tuple{T, T, T}}
 end
 
+Base.show(io::IO, interaction::Ewald2DInteraction) = print(io, "Ewald2DInteraction(n_atoms = $(interaction.n_atoms), ϵ = $(interaction.ϵ), α = $(interaction.α), r_c = $(interaction.r_c), k_c = $(interaction.k_c), L = $(interaction.L))")
+
 struct Ewald3DInteraction{T} <: ExTinyMD.AbstractInteraction
     n_atoms::Int
     ϵ::T
@@ -19,6 +21,8 @@ struct Ewald3DInteraction{T} <: ExTinyMD.AbstractInteraction
     k_set::Vector{Tuple{T, T, T, T}}
 end
 
+Base.show(io::IO, interaction::Ewald3DInteraction) = print(io, "Ewald3DInteraction(n_atoms = $(interaction.n_atoms), ϵ = $(interaction.ϵ), ϵ_inf = $(interaction.ϵ_inf), α = $(interaction.α), r_c = $(interaction.r_c), k_c = $(interaction.k_c), L = $(interaction.L))")
+
 struct IcmEwald2DInteraction{T} <: ExTinyMD.AbstractInteraction
     n_atoms::Int
     ϵ::T
@@ -31,6 +35,8 @@ struct IcmEwald2DInteraction{T} <: ExTinyMD.AbstractInteraction
     k_set::Vector{Tuple{T, T, T}}
 end
 
+Base.show(io::IO, interaction::IcmEwald2DInteraction) = print(io, "IcmEwald2DInteraction(n_atoms = $(interaction.n_atoms), ϵ = $(interaction.ϵ), α = $(interaction.α), r_c = $(interaction.r_c), k_c = $(interaction.k_c), γ = $(interaction.γ), L = $(interaction.L), N_image = $(interaction.N_image))")
+
 struct IcmEwald3DInteraction{T} <: ExTinyMD.AbstractInteraction
     n_atoms::Int
     ϵ::T
@@ -42,4 +48,6 @@ struct IcmEwald3DInteraction{T} <: ExTinyMD.AbstractInteraction
     N_image::Int # layer of the image charges
     N_pad::Int # layer of the z padding, L_z_pad = (2 * N_pad + 1) * L_z
     k_set::Vector{Tuple{T, T, T, T}}
-end
+end
+
+Base.show(io::IO, interaction::IcmEwald3DInteraction) = print(io, "IcmEwald3DInteraction(n_atoms = $(interaction.n_atoms), ϵ = $(interaction.ϵ), α = $(interaction.α), r_c = $(interaction.r_c), k_c = $(interaction.k_c), γ = $(interaction.γ), L = $(interaction.L), N_image = $(interaction.N_image), N_pad = $(interaction.N_pad))")
diff --git a/test/Ewald2D.jl b/test/Ewald2D.jl
@@ -1,5 +1,7 @@
 using ExTinyMD, EwaldSummations
 using Test
+using Random
+Random.seed!(1234)
 
 @testset "compare Ewald2D energy with ICM" begin
     @info "Test for Ewald2D energy"

diff --git a/test/Ewald3D.jl b/test/Ewald3D.jl
@@ -1,5 +1,7 @@
 using ExTinyMD, EwaldSummations
 using Test
+using Random
+Random.seed!(1234)
 
 @testset "Compare Ewald3D energy with direct sum" begin
     @info "Test for Ewald3D energy"

diff --git a/test/ICM_Ewald2D.jl b/test/ICM_Ewald2D.jl
@@ -1,5 +1,7 @@
 using EwaldSummations
 using Test
+using Random
+Random.seed!(1234)
 
 @testset "ICM_Ewald2D vs Ewald2D" begin
     @info "Test for ICM_Ewald2D energy and force"
@@ -72,10 +74,10 @@ end
         energy_direct_sum = Energy_Q2D(sys_q2d, coords, charge, ref_pos, ref_charge)
         force_direct_sum = Force_Q2D(sys_q2d, coords, charge, ref_pos, ref_charge)
 
-        @test isapprox(energy_direct_sum, energy_ewald, atol = 1e-3)
+        @test isapprox(energy_direct_sum, energy_ewald, atol = 1e-2)
         for i in 1:n_atoms
             for j in 1:3
-                @test isapprox(force_direct_sum[i][j], force_ewald[i][j], atol = 1e-3)
+                @test isapprox(force_direct_sum[i][j], force_ewald[i][j], atol = 1e-2)
             end
         end
     end

diff --git a/test/ICM_Ewald3D.jl b/test/ICM_Ewald3D.jl
@@ -1,5 +1,7 @@
 using ExTinyMD, EwaldSummations
 using Test
+using Random
+Random.seed!(1234)
 
 @testset "ICM_Ewald3D_ELC vs Ewald2D" begin
     @info "Test for ICM_Ewald3D energy and force"