ArrayType -> array_type

benchmark/benchmarks.jl

@@ -63,7 +63,7 @@ const starting_coords_f32 = [Float32.(c) for c in starting_coords]
 const starting_velocities_f32 = [Float32.(c) for c in starting_velocities]
 
 function test_sim(nl::Bool, parallel::Bool, f32::Bool,
-                  ArrayType::Type{AT}) where AT <: AbstractArray
+                  array_type::Type{AT}) where AT <: AbstractArray
     n_atoms = 400
     n_steps = 200
     atom_mass = f32 ? 10.0f0u"g/mol" : 10.0u"g/mol"
@@ -73,26 +73,26 @@ function test_sim(nl::Bool, parallel::Bool, f32::Bool,
     r0 = f32 ? 0.2f0u"nm" : 0.2u"nm"
     bonds = [HarmonicBond(k=k, r0=r0) for i in 1:(n_atoms ÷ 2)]
     specific_inter_lists = (InteractionList2Atoms(
-        ArrayType(Int32.(collect(1:2:n_atoms))),
-        ArrayType(Int32.(collect(2:2:n_atoms))),
-        ArrayType(bonds),
+        array_type(Int32.(collect(1:2:n_atoms))),
+        array_type(Int32.(collect(2:2:n_atoms))),
+        array_type(bonds),
     ),)
 
     neighbor_finder = NoNeighborFinder()
     cutoff = DistanceCutoff(f32 ? 1.0f0u"nm" : 1.0u"nm")
     pairwise_inters = (LennardJones(use_neighbors=false, cutoff=cutoff),)
     if nl
         neighbor_finder = DistanceNeighborFinder(
-            eligible=ArrayType(trues(n_atoms, n_atoms)),
+            eligible=array_type(trues(n_atoms, n_atoms)),
             n_steps=10,
             dist_cutoff=f32 ? 1.5f0u"nm" : 1.5u"nm",
         )
         pairwise_inters = (LennardJones(use_neighbors=true, cutoff=cutoff),)
     end
 
-    coords = ArrayType(deepcopy(f32 ? starting_coords_f32 : starting_coords))
-    velocities = ArrayType(deepcopy(f32 ? starting_velocities_f32 : starting_velocities))
-    atoms = ArrayType([Atom(charge=f32 ? 0.0f0 : 0.0, mass=atom_mass, σ=f32 ? 0.2f0u"nm" : 0.2u"nm",
+    coords = array_type(deepcopy(f32 ? starting_coords_f32 : starting_coords))
+    velocities = array_type(deepcopy(f32 ? starting_velocities_f32 : starting_velocities))
+    atoms = array_type([Atom(charge=f32 ? 0.0f0 : 0.0, mass=atom_mass, σ=f32 ? 0.2f0u"nm" : 0.2u"nm",
                             ϵ=f32 ? 0.2f0u"kJ * mol^-1" : 0.2u"kJ * mol^-1") for i in 1:n_atoms])
 
     sys = System(

benchmark/protein.jl

@@ -11,7 +11,7 @@ const data_dir = normpath(dirname(pathof(Molly)), "..", "data")
 const ff_dir = joinpath(data_dir, "force_fields")
 const openmm_dir = joinpath(data_dir, "openmm_6mrr")
 
-function setup_system(ArrayType::AbstractArray, f32::Bool, units::Bool)
+function setup_system(array_type::AbstractArray, f32::Bool, units::Bool)
     T = f32 ? Float32 : Float64
     ff = MolecularForceField(
         T,
@@ -27,7 +27,7 @@ function setup_system(ArrayType::AbstractArray, f32::Bool, units::Bool)
     sys = System(
         joinpath(data_dir, "6mrr_equil.pdb"),
         ff;
-        velocities=ArrayType(velocities),
+        velocities=array_type(velocities),
         units=units,
         gpu=gpu,
         dist_cutoff=(units ? dist_cutoff * u"nm" : dist_cutoff),

src/interactions/implicit_solvent.jl

@@ -412,10 +412,10 @@ function ImplicitSolventOBC(atoms::AbstractArray{Atom{TY, M, T, D, E}},
     end
 
     if isa(atoms, AbstractGPUArray)
-        ArrayType = get_array_type(atoms)
-        or = ArrayType(offset_radii)
-        sor = ArrayType(scaled_offset_radii)
-        is, js = ArrayType(inds_i), ArrayType(inds_j)
+        array_type = get_array_type(atoms)
+        or = array_type(offset_radii)
+        sor = array_type(scaled_offset_radii)
+        is, js = array_type(inds_i), array_type(inds_j)
     else
         or = offset_radii
         sor = scaled_offset_radii
@@ -565,12 +565,12 @@ function ImplicitSolventGBN2(atoms::AbstractArray{Atom{TY, M, T, D, E}},
     end
 
     if isa(atoms, AbstractGPUArray)
-        ArrayType = get_array_type(atoms)
-        or = ArrayType(offset_radii)
-        sor = ArrayType(scaled_offset_radii)
-        is, js = ArrayType(inds_i), ArrayType(inds_j)
-        d0s, m0s = ArrayType(table_d0), ArrayType(table_m0)
-        αs, βs, γs = ArrayType(αs_cpu), ArrayType(βs_cpu), ArrayType(γs_cpu)
+        array_type = get_array_type(atoms)
+        or = array_type(offset_radii)
+        sor = array_type(scaled_offset_radii)
+        is, js = array_type(inds_i), array_type(inds_j)
+        d0s, m0s = array_type(table_d0), array_type(table_m0)
+        αs, βs, γs = array_type(αs_cpu), array_type(βs_cpu), array_type(γs_cpu)
     else
         or = offset_radii
         sor = scaled_offset_radii

src/setup.jl

@@ -428,7 +428,7 @@ are not available when reading Gromacs files.
 - `loggers=()`: the loggers that record properties of interest during a
     simulation.
 - `units::Bool=true`: whether to use Unitful quantities.
-- `ArrayType::AbstractArray = Array`: The ArrayType desired for the simulation
+- `array_type::AbstractArray = Array`: The array_type desired for the simulation
    (for GPU support, use CuArray or ROCArray)
 - `dist_cutoff=1.0u"nm"`: cutoff distance for long-range interactions.
 - `dist_neighbors=1.2u"nm"`: cutoff distance for the neighbor list, should be
@@ -452,7 +452,7 @@ function System(coord_file::AbstractString,
                 velocities=nothing,
                 loggers=(),
                 units::Bool=true,
-                ArrayType::Type{AT} where AT <: AbstractArray = Array,
+                array_type::Type{AT} where AT <: AbstractArray = Array,
                 dist_cutoff=units ? 1.0u"nm" : 1.0,
                 dist_neighbors=units ? 1.2u"nm" : 1.2,
                 center_coords::Bool=true,
@@ -824,9 +824,9 @@ function System(coord_file::AbstractString,
     specific_inter_array = []
     if length(bonds.is) > 0
         push!(specific_inter_array, InteractionList2Atoms(
-            ArrayType(bonds.is),
-            ArrayType(bonds.js),
-            ArrayType([bonds.inters...]),
+            array_type(bonds.is),
+            array_type(bonds.js),
+            array_type([bonds.inters...]),
             bonds.types,
         ))
         topology = MolecularTopology(bonds.is, bonds.js, n_atoms)
@@ -835,30 +835,30 @@ function System(coord_file::AbstractString,
     end
     if length(angles.is) > 0
         push!(specific_inter_array, InteractionList3Atoms(
-            ArrayType(angles.is),
-            ArrayType(angles.js),
-            ArrayType(angles.ks),
-            ArrayType([angles.inters...]),
+            array_type(angles.is),
+            array_type(angles.js),
+            array_type(angles.ks),
+            array_type([angles.inters...]),
             angles.types,
         ))
     end
     if length(torsions.is) > 0
         push!(specific_inter_array, InteractionList4Atoms(
-            ArrayType(torsions.is),
-            ArrayType(torsions.js),
-            ArrayType(torsions.ks),
-            ArrayType(torsions.ls),
-            ArrayType(torsion_inters_pad),
+            array_type(torsions.is),
+            array_type(torsions.js),
+            array_type(torsions.ks),
+            array_type(torsions.ls),
+            array_type(torsion_inters_pad),
             torsions.types,
         ))
     end
     if length(impropers.is) > 0
         push!(specific_inter_array, InteractionList4Atoms(
-            ArrayType(impropers.is),
-            ArrayType(impropers.js),
-            ArrayType(impropers.ks),
-            ArrayType(impropers.ls),
-            ArrayType(improper_inters_pad),
+            array_type(impropers.is),
+            array_type(impropers.js),
+            array_type(impropers.ks),
+            array_type(impropers.ls),
+            array_type(improper_inters_pad),
             impropers.types,
         ))
     end
@@ -887,10 +887,10 @@ function System(coord_file::AbstractString,
     end
     coords = wrap_coords.(coords, (boundary_used,))
 
-    if (ArrayType <: AbstractGPUArray) || !use_cell_list
+    if (array_type <: AbstractGPUArray) || !use_cell_list
         neighbor_finder = DistanceNeighborFinder(
-            eligible=(ArrayType(eligible)),
-            special=(ArrayType(special)),
+            eligible=(array_type(eligible)),
+            special=(array_type(special)),
             n_steps=10,
             dist_cutoff=T(dist_neighbors),
         )
@@ -905,8 +905,8 @@ function System(coord_file::AbstractString,
         )
     end
 
-    atoms = ArrayType([atoms_abst...])
-    coords_dev = ArrayType(coords)
+    atoms = array_type([atoms_abst...])
+    coords_dev = array_type(coords)
 
     if isnothing(velocities)
         if units
@@ -961,7 +961,7 @@ function System(T::Type,
                 velocities=nothing,
                 loggers=(),
                 units::Bool=true,
-                ArrayType::Type{AT} where AT <: AbstractArray = Array,
+                array_type::Type{AT} where AT <: AbstractArray = Array,
                 dist_cutoff=units ? 1.0u"nm" : 1.0,
                 dist_neighbors=units ? 1.2u"nm" : 1.2,
                 center_coords::Bool=true,
@@ -1242,9 +1242,9 @@ function System(T::Type,
     specific_inter_array = []
     if length(bonds.is) > 0
         push!(specific_inter_array, InteractionList2Atoms(
-            ArrayType(bonds.is),
-            ArrayType(bonds.js),
-            ArrayType([bonds.inters...]),
+            array_type(bonds.is),
+            array_type(bonds.js),
+            array_type([bonds.inters...]),
             bonds.types,
         ))
         topology = MolecularTopology(bonds.is, bonds.js, n_atoms)
@@ -1253,29 +1253,29 @@ function System(T::Type,
     end
     if length(angles.is) > 0
         push!(specific_inter_array, InteractionList3Atoms(
-            ArrayType(angles.is),
-            ArrayType(angles.js),
-            ArrayType(angles.ks),
-            ArrayType([angles.inters...]),
+            array_type(angles.is),
+            array_type(angles.js),
+            array_type(angles.ks),
+            array_type([angles.inters...]),
             angles.types,
         ))
     end
     if length(torsions.is) > 0
         push!(specific_inter_array, InteractionList4Atoms(
-            ArrayType(torsions.is),
-            ArrayType(torsions.js),
-            ArrayType(torsions.ks),
-            ArrayType(torsions.ls),
-            ArrayType([torsions.inters...]),
+            array_type(torsions.is),
+            array_type(torsions.js),
+            array_type(torsions.ks),
+            array_type(torsions.ls),
+            array_type([torsions.inters...]),
             torsions.types,
         ))
     end
     specific_inter_lists = tuple(specific_inter_array...)
 
-    if ArrayType <: AbstractGPUArray || !use_cell_list
+    if array_type <: AbstractGPUArray || !use_cell_list
         neighbor_finder = DistanceNeighborFinder(
-            eligible=(ArrayType(eligible)),
-            special=(ArrayType(special)),
+            eligible=(array_type(eligible)),
+            special=(array_type(special)),
             n_steps=10,
             dist_cutoff=T(dist_neighbors),
         )
@@ -1290,8 +1290,8 @@ function System(T::Type,
         )
     end
 
-    atoms = ArrayType([atoms_abst...])
-    coords_dev = ArrayType(coords)
+    atoms = array_type([atoms_abst...])
+    coords_dev = array_type(coords)
 
     if isnothing(velocities)
         if units

src/spatial.jl

@@ -876,8 +876,8 @@ function molecule_centers(coords::AbstractArray{SVector{D, C}}, boundary, topolo
 end
 
 function molecule_centers(coords::AbstractGPUArray, boundary, topology)
-    ArrayType = get_array_type(coords)
-    return ArrayType(molecule_centers(Array(coords), boundary, topology))
+    array_type = get_array_type(coords)
+    return array_type(molecule_centers(Array(coords), boundary, topology))
 end
 
 # Allows scaling multiple vectors at once by broadcasting this function

src/types.jl

@@ -183,23 +183,23 @@ function Base.:+(il1::InteractionList4Atoms{I, T}, il2::InteractionList4Atoms{I,
     )
 end
 
-function inject_interaction_list(inter::InteractionList1Atoms, params_dic, ArrayType)
-    inters_grad = ArrayType(inject_interaction.(Array(inter.inters), inter.types, (params_dic,)))
+function inject_interaction_list(inter::InteractionList1Atoms, params_dic, array_type)
+    inters_grad = array_type(inject_interaction.(Array(inter.inters), inter.types, (params_dic,)))
     InteractionList1Atoms(inter.is, inters_grad, inter.types)
 end
 
-function inject_interaction_list(inter::InteractionList2Atoms, params_dic, ArrayType)
-    inters_grad = ArrayType(inject_interaction.(Array(inter.inters), inter.types, (params_dic,)))
+function inject_interaction_list(inter::InteractionList2Atoms, params_dic, array_type)
+    inters_grad = array_type(inject_interaction.(Array(inter.inters), inter.types, (params_dic,)))
     InteractionList2Atoms(inter.is, inter.js, inters_grad, inter.types)
 end
 
-function inject_interaction_list(inter::InteractionList3Atoms, params_dic, ArrayType)
-    inters_grad = ArrayType(inject_interaction.(Array(inter.inters), inter.types, (params_dic,)))
+function inject_interaction_list(inter::InteractionList3Atoms, params_dic, array_type)
+    inters_grad = array_type(inject_interaction.(Array(inter.inters), inter.types, (params_dic,)))
     InteractionList3Atoms(inter.is, inter.js, inter.ks, inters_grad, inter.types)
 end
 
-function inject_interaction_list(inter::InteractionList4Atoms, params_dic, ArrayType)
-    inters_grad = ArrayType(inject_interaction.(Array(inter.inters), inter.types, (params_dic,)))
+function inject_interaction_list(inter::InteractionList4Atoms, params_dic, array_type)
+    inters_grad = array_type(inject_interaction.(Array(inter.inters), inter.types, (params_dic,)))
     InteractionList4Atoms(inter.is, inter.js, inter.ks, inter.ls, inters_grad, inter.types)
 end
 

test/basic.jl

@@ -176,16 +176,16 @@
     @test mcs == [SVector(0.05, 0.0), SVector(1.0, 1.0)]
 
     ff = MolecularForceField(joinpath.(ff_dir, ["ff99SBildn.xml", "tip3p_standard.xml", "his.xml"])...)
-    for ArrayType in array_list
-        sys = System(joinpath(data_dir, "6mrr_equil.pdb"), ff; ArrayType=ArrayType, use_cell_list=false)
+    for array_type in array_list
+        sys = System(joinpath(data_dir, "6mrr_equil.pdb"), ff; array_type=array_type, use_cell_list=false)
         mcs = molecule_centers(sys.coords, sys.boundary, sys.topology)
         @test isapprox(Array(mcs)[1], mean(sys.coords[1:1170]); atol=0.08u"nm")
 
         # Mark all pairs as ineligible for pairwise interactions and check that the
         #   potential energy from the specific interactions does not change on scaling
         no_nbs = falses(length(sys), length(sys))
         sys.neighbor_finder = DistanceNeighborFinder(
-            eligible=(ArrayType(no_nbs)),
+            eligible=(array_type(no_nbs)),
             dist_cutoff=1.0u"nm",
         )
         coords_start = copy(sys.coords)
@@ -312,7 +312,7 @@ end
 
     if run_cuda_tests
         sys_gpu = System(joinpath(data_dir, "6mrr_equil.pdb"), ff;
-                         ArrayType=CuArray)
+                         array_type=CuArray)
         for neighbor_finder in (DistanceNeighborFinder,)
             nf_gpu = neighbor_finder(
                 eligible=sys_gpu.neighbor_finder.eligible,
@@ -330,7 +330,7 @@ end
 
     if run_rocm_tests
         sys_gpu = System(joinpath(data_dir, "6mrr_equil.pdb"), ff;
-                         ArrayType=ROCArray)
+                         array_type=ROCArray)
         for neighbor_finder in (DistanceNeighborFinder,)
             nf_gpu = neighbor_finder(
                 eligible=sys_gpu.neighbor_finder.eligible,

test/energy_conservation.jl

@@ -6,7 +6,7 @@ using CUDA
 using Test
 
 @testset "Lennard-Jones energy conservation" begin
-    function test_energy_conservation(ArrayType::AbstractArray, n_threads::Integer, n_steps::Integer)
+    function test_energy_conservation(array_type::AbstractArray, n_threads::Integer, n_steps::Integer)
         n_atoms = 2_000
         atom_mass = 40.0u"g/mol"
         temp = 1.0u"K"
@@ -26,8 +26,8 @@ using Test
             coords = place_atoms(n_atoms, boundary; min_dist=0.6u"nm")
 
             sys = System(
-                atoms=(ArrayType(atoms) : atoms),
-                coords=(ArrayType(coords) : coords),
+                atoms=(array_type(atoms) : atoms),
+                coords=(array_type(coords) : coords),
                 boundary=boundary,
                 pairwise_inters=(LennardJones(cutoff=cutoff, use_neighbors=false),),
                 loggers=(

test/gradients.jl

@@ -251,13 +251,13 @@ end
 end
 
 @testset "Differentiable protein" begin
-    function create_sys(ArrayType)
+    function create_sys(array_type)
         ff = MolecularForceField(joinpath.(ff_dir, ["ff99SBildn.xml", "his.xml"])...; units=false)
         return System(
             joinpath(data_dir, "6mrr_nowater.pdb"),
             ff;
             units=false,
-            ArrayType=ArrayType,
+            array_type=array_type,
             implicit_solvent="gbn2",
             kappa=0.7,
         )