Merge pull request #40 from TheDisorderedOrganization/cleanup

Clean up the code with new code version

Author: romainljsimon

src/IO/IO.jl

@@ -20,7 +20,7 @@ function Arianna.write_system(io, system::Particles)
     println(io, "\tCell: $(system.box)")
     println(io, "\tDensity: $(system.density)")
     println(io, "\tTemperature: $(system.temperature)")
-    println(io, "\tCell list: " * replace(string(typeof(system.cell_list)), r"\{.*" => ""))
+    println(io, "\tNeighbour list: " * replace(string(typeof(system.neighbour_list)), r"\{.*" => ""))
     return nothing
 end
 

src/ParticlesMC.jl

@@ -7,7 +7,7 @@ abstract type Particles <: AriannaSystem end
 
 
 include("utils.jl")
-include("cell_list.jl")
+include("neighbours.jl")
 include("models.jl")
 include("molecules.jl")
 include("atoms.jl")
@@ -18,7 +18,7 @@ get_species(system::Particles, i::Int) = @inbounds system.species[i]
 get_model(system::Particles, i::Int, j::Int) = @inbounds system.model_matrix[get_species(system, i), get_species(system, j)]
 get_local_energy(system::Particles, i::Int) = @inbounds system.local_energy[i]
 get_box(system::Particles) = system.box
-get_neighbour_list(system::Particles) = system.cell_list
+get_neighbour_list(system::Particles) = system.neighbour_list
 Base.length(system::Particles) = system.N
 Base.eachindex(system::Particles) = Base.OneTo(length(system))
 Base.getindex(system::Atoms, i::Int) = system.position[i], system.species[i], system.local_energy[i]
@@ -28,16 +28,8 @@ function Base.iterate(system::Union{Atoms, Molecules}, state=1)
     return (system.position[state], state + 1)  # Return element & next state
 end
 
-function compute_local_energy(system::Particles, i)
-    return compute_local_energy(system, i, system.cell_list)
-end
-
-function destroy_particle!(system::Particles, i)
-    return destroy_particle!(system, i, system.cell_list)
-end
-
-function create_particle!(system::Particles, i)
-    return destroy_particle!(system, i, system.cell_list)
+function compute_energy_particle(system::Particles, i)
+    return compute_energy_particle(system, i, system.neighbour_list)
 end
 
 

src/atoms.jl

@@ -9,7 +9,7 @@ struct Atoms{D, Q, V<:AbstractVector, C<:NeighbourList, H, T<:AbstractFloat, SM<
     d::Int
     box::SVector{D,T}
     local_energy::MVector{Q, T}
-    cell_list::C
+    neighbour_list::C
     species_list::H
 end
 
@@ -23,11 +23,11 @@ function System(position, species, density::T, temperature::T, model_matrix; lis
     local_energy = MVector{N, T}(zeros(T, N))
     indices = MVector{N, Bool}(falses(N))
     maxcut = maximum([model.rcut for model in model_matrix])
-    cell_list = list_type(box, maxcut, N)
+    neighbour_list = list_type(box, maxcut, N)
     species_list = isa(species[1], Integer) ? SpeciesList(species) : nothing
-    system = Atoms(position, species, density, energy, temperature, model_matrix, N, d, box, local_energy, cell_list, species_list)
-    build_cell_list!(system)
-    system.local_energy .= [compute_local_energy(system, i) for i in eachindex(system)]
+    system = Atoms(position, species, density, energy, temperature, model_matrix, N, d, box, local_energy, neighbour_list, species_list)
+    build_neighbour_list!(system)
+    system.local_energy .= [compute_energy_particle(system, i) for i in eachindex(system)]
     system.energy[1] = sum(system.local_energy) / 2
     return system
 end
@@ -47,11 +47,11 @@ function compute_energy_ij(system::Atoms, position_i, position_j, model_ij::Mode
     return potential(r2, model_ij)
 end
 
-function compute_local_energy(system::Atoms, i)
-    return compute_local_energy(system, i, system.cell_list)
+function compute_energy_particle(system::Atoms, i)
+    return compute_energy_particle(system, i, system.neighbour_list)
 end
 
-function compute_local_energy(system::Atoms, i, ::EmptyList)
+function compute_energy_particle(system::Atoms, i, ::EmptyList)
     energy_i = zero(typeof(system.density))
     position_i = get_position(system, i)
     for (j, _) in enumerate(system)
@@ -61,140 +61,37 @@ function compute_local_energy(system::Atoms, i, ::EmptyList)
 end
 
 
-function destroy_particle!(system::Atoms, i, ::EmptyList)
+function compute_energy_particle(system::Atoms, i, neighbour_list::CellList)
     energy_i = zero(typeof(system.density))
     position_i = get_position(system, i)
-    # Loop over particles
-    @inbounds for (j, _) in enumerate(system)
-        energy_ij = check_compute_energy_ij(system, i, j, position_i)
-        energy_i += energy_ij
-    end
-    return energy_i
-end
-
-function create_particle!(system::Atoms, i, ::EmptyList)
-    energy_i = zero(typeof(system.density))
-    position_i = get_position(system, i)
-    # Loop over particles
-    @inbounds for (j, position_j) in enumerate(system)
-        energy_ij = check_compute_energy_ij(system, i, j, position_i)
-        energy_i += energy_ij
-    end
-    return energy_i
-end
+    c = get_cell_index(position_i, neighbour_list)
+    neighbour_cells = neighbour_list.neighbour_cells[c]
 
-function compute_local_energy(system::Atoms, i, cell_list::CellList)
-    energy_i = zero(typeof(system.density))
-    position_i = get_position(system, i)
-    mc = get_cell(position_i, cell_list)
-    # Scan the neighbourhood of cell mc (including itself)
-    @inbounds for mc2 in Iterators.product(map(x -> x-1:x+1, mc)...)
-        # Calculate the scalar cell index of the neighbour cell (with PBC)
-        c2 = cell_index(cell_list, mc2)
-        # Scan atoms in cell c2
-        @inbounds for j in cell_list.cells[c2]
-            energy_i += check_compute_energy_ij(system, i, j, position_i)
-        end
-    end
-    return energy_i
-end
-
-# With linked list
-function destroy_particle!(system::Atoms, i, cell_list::CellList)
-    # Get cell of particle i
-    energy_i = zero(typeof(system.density))
-    position_i = get_position(system, i)
-    mc = get_cell(position_i, cell_list)
-    # Scan the neighbourhood of cell mc (including itself)
-    @inbounds for mc2 in Iterators.product(map(x -> x-1:x+1, mc)...)
-        # Calculate the scalar cell index of the neighbour cell (with PBC)
-        c2 = cell_index(cell_list, mc2)
-        # Scan atoms in cell c2
-        neighbours = cell_list.cells[c2]
-        @inbounds for j in neighbours
-            energy_ij = check_compute_energy_ij(system, i, j, position_i)
-            energy_i += energy_ij
-        end
-    end
-    return energy_i
-end
-
-function create_particle!(system::Atoms, i, cell_list::CellList)
-    energy_i = zero(typeof(system.density))
-    # Get cell of particle i
-    position_i = get_position(system, i)
-    mc = get_cell(position_i, cell_list)
     # Scan the neighbourhood of cell mc (including itself)
-    @inbounds for mc2 in Iterators.product(map(x -> x-1:x+1, mc)...)
-        # Calculate the scalar cell index of the neighbour cell (with PBC)
-        c2 = cell_index(cell_list, mc2)
+    @inbounds for c2 in neighbour_cells
         # Scan atoms in cell c2
-        neighbours = cell_list.cells[c2]
+        neighbours = neighbour_list.cells[c2]
         @inbounds for j in neighbours
-            energy_ij = check_compute_energy_ij(system, i, j, position_i)
-            energy_i += energy_ij
-        end
-    end
-    return energy_i
-end
-
-
-function compute_local_energy(system::Atoms, i, cell_list::LinkedList)
-    energy_i = zero(typeof(system.density))
-    # Get cell of particle i
-    position_i = get_position(system, i)
-    mc = get_cell(position_i, cell_list)
-    # Scan the neighbourhood of cell mc (including itself)
-    @inbounds for mc2 in Iterators.product(map(x -> x-1:x+1, mc)...)
-        # Calculate the scalar cell index of the neighbour cell (with PBC)
-        c2 = cell_index(cell_list, mc2)
-        # Scan atoms in cell c2
-        j = cell_list.head[c2]
-        while (j != -1)
-            energy_ij = check_compute_energy_ij(system, i, j, position_i)
-            energy_i += energy_ij
-            j = cell_list.list[j]
-        end
-    end
-    return energy_i
-end
-
-
-function destroy_particle!(system::Atoms, i, cell_list::LinkedList)
-    energy_i = zero(typeof(system.density))
-    # Get cell of particle i
-    position_i = get_position(system, i)
-    mc = get_cell(position_i, cell_list)
-    # Scan the neighbourhood of cell mc (including itself)
-    @inbounds for mc2 in Iterators.product(map(x -> x-1:x+1, mc)...)
-        # Calculate the scalar cell index of the neighbour cell (with PBC)
-        c2 = cell_index(cell_list, mc2)
-        # Scan atoms in cell c2
-        j = cell_list.head[c2]
-        while (j != -1)
-            energy_ij = check_compute_energy_ij(system, i, j, position_i)
-            energy_i += energy_ij
-            j = cell_list.list[j]
+            energy_i += check_compute_energy_ij(system, i, j, position_i)
         end
     end
     return energy_i
 end
 
-function create_particle!(system::Atoms, i, cell_list::LinkedList)
+function compute_energy_particle(system::Atoms, i, neighbour_list::LinkedList)
     energy_i = zero(typeof(system.density))
     # Get cell of particle i
     position_i = get_position(system, i)
-    mc = get_cell(position_i, cell_list)
+    c = get_cell_index(position_i, neighbour_list)
+    neighbour_cells = neighbour_list.neighbour_cells[c]
     # Scan the neighbourhood of cell mc (including itself)
-    @inbounds for mc2 in Iterators.product(map(x -> x-1:x+1, mc)...)
-        # Calculate the scalar cell index of the neighbour cell (with PBC)
-        c2 = cell_index(cell_list, mc2)
+    @inbounds for c2 in neighbour_cells
         # Scan atoms in cell c2
-        j = cell_list.head[c2]
+        j = neighbour_list.head[c2]
         while (j != -1)
             energy_ij = check_compute_energy_ij(system, i, j, position_i)
             energy_i += energy_ij
-            j = cell_list.list[j]
+            j = neighbour_list.list[j]
         end
     end
     return energy_i