Merge branch 'dev' into release-0.2

trixi-framework · Jun 27, 2024 · 0382fc8 · 0382fc8
2 parents cb84f30 + 2326d03
commit 0382fc8
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diff --git a/Project.toml b/Project.toml
@@ -39,7 +39,7 @@ GPUArrays = "9, 10"
 JSON = "0.21"
 KernelAbstractions = "0.9"
 MuladdMacro = "0.2"
-PointNeighbors = "0.2.3"
+PointNeighbors = "0.3"
 Polyester = "0.7.5"
 RecipesBase = "1"
 Reexport = "1"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,9 +1,11 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+PointNeighbors = "1c4d5385-0a27-49de-8e2c-43b175c8985c"
 TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
 
 [compat]
 Documenter = "1"
 OrdinaryDiffEq = "6"
+PointNeighbors = "0.3"
 TrixiBase = "0.1"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,6 +1,7 @@
 using Documenter
 using TrixiParticles
 using TrixiBase
+using PointNeighbors
 
 # Get TrixiParticles.jl root directory
 trixiparticles_root_dir = dirname(@__DIR__)
@@ -129,6 +130,7 @@ makedocs(sitename="TrixiParticles.jl",
  "Time Integration" => "time_integration.md",
  "Callbacks" => "callbacks.md",
  "TrixiBase.jl API Reference" => "reference-trixibase.md",
+ "PointNeighbors.jl API Reference" => "reference-pointneighbors.md",
  ],
  "Authors" => "authors.md",
  "Contributing" => "contributing.md",

diff --git a/docs/src/general/neighborhood_search.md b/docs/src/general/neighborhood_search.md
@@ -6,31 +6,30 @@ We provide several implementations in the package
 See the docs of this package for an overview and a comparison of different implementations.
 
 !!! note "Usage"
- To run a simulation with a neighborhood search implementation, just pass the type
- to the constructor of the [`Semidiscretization`](@ref):
+ To run a simulation with a neighborhood search implementation, pass a template of the
+ neighborhood search to the constructor of the [`Semidiscretization`](@ref).
+ A template is just an empty neighborhood search with search radius `0.0`.
+ See [`copy_neighborhood_search`](@ref) and the examples below for more details.
  ```jldoctest semi_example; output=false, setup = :(using TrixiParticles; trixi_include(@__MODULE__, joinpath(examples_dir(), "fluid", "hydrostatic_water_column_2d.jl"), sol=nothing); system1 = fluid_system; system2 = boundary_system)
  semi = Semidiscretization(system1, system2,
- neighborhood_search=GridNeighborhoodSearch)
+ neighborhood_search=PrecomputedNeighborhoodSearch{2}())
 
  # output
  ┌──────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ Semidiscretization │
  │ ══════════════════ │
  │ #spatial dimensions: ………………………… 2 │
  │ #systems: ……………………………………………………… 2 │
- │ neighborhood search: ………………………… GridNeighborhoodSearch  │
+ │ neighborhood search: ………………………… PrecomputedNeighborhoodSearch │
  │ total #particles: ………………………………… 636 │
  └──────────────────────────────────────────────────────────────────────────────────────────────────┘
  ```
- The keyword arguments `periodic_box_min_corner` and `periodic_box_max_corner` mentioned
- in the PointNeighbors.jl docs can also be passed to the
- [`Semidiscretization`](@ref) and will internally be forwarded to the neighborhood search.
- See the docs of [`Semidiscretization`](@ref) for more details.
+ The keyword argument `periodic_box` in the neighborhood search constructors can be used
+ to define a periodic domain. See the PointNeighbors.jl docs for more details.
  ```jldoctest semi_example; output = false
+ periodic_box = PeriodicBox(min_corner=[0.0, -0.25], max_corner=[1.0, 0.75])
  semi = Semidiscretization(system1, system2,
-  neighborhood_search=GridNeighborhoodSearch,
-  periodic_box_min_corner=[0.0, -0.25],
-  periodic_box_max_corner=[1.0, 0.75])
+  neighborhood_search=GridNeighborhoodSearch{2}(; periodic_box))
 
  # output
  ┌──────────────────────────────────────────────────────────────────────────────────────────────────┐

diff --git a/docs/src/reference-pointneighbors.md b/docs/src/reference-pointneighbors.md
@@ -0,0 +1,9 @@
+# PointNeighbors.jl API
+
+```@meta
+CurrentModule = PointNeighbors
+```
+
+```@autodocs
+Modules = [PointNeighbors]
+```
diff --git a/examples/dem/rectangular_tank_2d.jl b/examples/dem/rectangular_tank_2d.jl
@@ -30,8 +30,7 @@ boundary_system = BoundaryDEMSystem(tank.boundary, 10e7)
 # ==========================================================================================
 # ==== Simulation
 
-semi = Semidiscretization(rock_system, boundary_system,
- neighborhood_search=GridNeighborhoodSearch)
+semi = Semidiscretization(rock_system, boundary_system)
 
 tspan = (0.0, 5.0)
 ode = semidiscretize(semi, tspan)

diff --git a/examples/fluid/dam_break_2d.jl b/examples/fluid/dam_break_2d.jl
@@ -74,8 +74,7 @@ boundary_system = BoundarySPHSystem(tank.boundary, boundary_model, adhesion_coef
 # ==========================================================================================
 # ==== Simulation
 semi = Semidiscretization(fluid_system, boundary_system,
- neighborhood_search=GridNeighborhoodSearch,
- threaded_nhs_update=true)
+ neighborhood_search=GridNeighborhoodSearch{2}(threaded_update=true))
 ode = semidiscretize(semi, tspan, data_type=nothing)
 
 info_callback = InfoCallback(interval=100)

diff --git a/examples/fluid/periodic_channel_2d.jl b/examples/fluid/periodic_channel_2d.jl
@@ -56,9 +56,10 @@ boundary_system = BoundarySPHSystem(tank.boundary, boundary_model)
 
 # ==========================================================================================
 # ==== Simulation
-semi = Semidiscretization(fluid_system, boundary_system,
- periodic_box_min_corner=[0.0, -0.25],
- periodic_box_max_corner=[1.0, 0.75])
+periodic_box = PeriodicBox(min_corner=[0.0, -0.25], max_corner=[1.0, 0.75])
+neighborhood_search = GridNeighborhoodSearch{2}(; periodic_box)
+
+semi = Semidiscretization(fluid_system, boundary_system; neighborhood_search)
 ode = semidiscretize(semi, tspan)
 
 info_callback = InfoCallback(interval=100)

diff --git a/examples/n_body/n_body_system.jl b/examples/n_body/n_body_system.jl
@@ -2,7 +2,7 @@ using TrixiParticles
 using LinearAlgebra
 
 # The second type parameter of `System` can't be `Nothing`, or TrixiParticles will launch
-# GPU kernel for `for_particle_neighbor` loops.
+# GPU kernel for `foreach_point_neighbor` loops.
 struct NBodySystem{NDIMS, ELTYPE <: Real} <: TrixiParticles.System{NDIMS, 0}
  initial_condition :: InitialCondition{ELTYPE}
  mass :: Array{ELTYPE, 1} # [particle]
@@ -39,7 +39,7 @@ function TrixiParticles.update_nhs!(neighborhood_search,
  u_system, u_neighbor)
  TrixiParticles.PointNeighbors.update!(neighborhood_search,
  u_system, u_neighbor,
- particles_moving=(true, true))
+ points_moving=(true, true))
 end
 
 function TrixiParticles.compact_support(system::NBodySystem,
@@ -59,10 +59,10 @@ function TrixiParticles.interact!(dv, v_particle_system, u_particle_system,
  neighbor_coords = TrixiParticles.current_coordinates(u_neighbor_system, neighbor_system)
 
  # Loop over all pairs of particles and neighbors within the kernel cutoff.
- TrixiParticles.for_particle_neighbor(particle_system, neighbor_system,
- system_coords, neighbor_coords,
- neighborhood_search) do particle, neighbor,
- pos_diff, distance
+ TrixiParticles.foreach_point_neighbor(particle_system, neighbor_system,
+  system_coords, neighbor_coords,
+  neighborhood_search) do particle, neighbor,
+  pos_diff, distance
  # Only consider particles with a distance > 0.
  distance < sqrt(eps()) && return
 

diff --git a/src/TrixiParticles.jl b/src/TrixiParticles.jl
@@ -25,8 +25,9 @@ using StrideArrays: PtrArray, StaticInt
 using TimerOutputs: TimerOutput, TimerOutputs, print_timer, reset_timer!
 using TrixiBase: trixi_include, @trixi_timeit, timer, timeit_debug_enabled,
  disable_debug_timings, enable_debug_timings
-@reexport using PointNeighbors: TrivialNeighborhoodSearch, GridNeighborhoodSearch
-using PointNeighbors: PointNeighbors, for_particle_neighbor
+@reexport using PointNeighbors: TrivialNeighborhoodSearch, GridNeighborhoodSearch,
+ PrecomputedNeighborhoodSearch, PeriodicBox
+using PointNeighbors: PointNeighbors, foreach_point_neighbor, copy_neighborhood_search
 using WriteVTK: vtk_grid, MeshCell, VTKCellTypes, paraview_collection, vtk_save
 
 # `util.jl` depends on the `GPUSystem` type defined in `system.jl`

diff --git a/src/general/corrections.jl b/src/general/corrections.jl
@@ -193,10 +193,10 @@ function compute_shepard_coeff!(system, system_coords, v_ode, u_ode, semi,
  neighborhood_search = get_neighborhood_search(system, neighbor_system, semi)
 
  # Loop over all pairs of particles and neighbors within the kernel cutoff
- for_particle_neighbor(system, neighbor_system, system_coords,
- neighbor_coords, neighborhood_search,
- particles=eachparticle(system)) do particle, neighbor,
-  pos_diff, distance
+ foreach_point_neighbor(system, neighbor_system, system_coords,
+  neighbor_coords, neighborhood_search,
+  points=eachparticle(system)) do particle, neighbor,
+ pos_diff, distance
  rho_b = particle_density(v_neighbor_system, neighbor_system, neighbor)
  m_b = hydrodynamic_mass(neighbor_system, neighbor)
  volume = m_b / rho_b
@@ -255,11 +255,10 @@ function compute_correction_values!(system,
  neighborhood_search = get_neighborhood_search(system, neighbor_system, semi)
 
  # Loop over all pairs of particles and neighbors within the kernel cutoff
- for_particle_neighbor(system, neighbor_system, system_coords,
- neighbor_coords,
- neighborhood_search,
- particles=eachparticle(system)) do particle, neighbor,
- pos_diff, distance
+ foreach_point_neighbor(system, neighbor_system, system_coords,
+ neighbor_coords, neighborhood_search,
+ points=eachparticle(system)) do particle, neighbor,
+ pos_diff, distance
  rho_b = particle_density(v_neighbor_system, neighbor_system, neighbor)
  m_b = hydrodynamic_mass(neighbor_system, neighbor)
  volume = m_b / rho_b
@@ -361,11 +360,9 @@ function compute_gradient_correction_matrix!(corr_matrix, neighborhood_search,
  set_zero!(corr_matrix)
 
  # Loop over all pairs of particles and neighbors within the kernel cutoff.
- for_particle_neighbor(system, system,
- coordinates, coordinates,
- neighborhood_search;
- particles=eachparticle(system)) do particle, neighbor,
- pos_diff, distance
+ foreach_point_neighbor(system, system, coordinates, coordinates, neighborhood_search;
+ points=eachparticle(system)) do particle, neighbor,
+ pos_diff, distance
  volume = mass[neighbor] / density_fun(neighbor)
 
  grad_kernel = smoothing_kernel_grad(system, pos_diff, distance)
@@ -397,12 +394,10 @@ function compute_gradient_correction_matrix!(corr_matrix::AbstractArray, system,
  neighbor_coords = current_coordinates(u_neighbor_system, neighbor_system)
  neighborhood_search = get_neighborhood_search(system, neighbor_system, semi)
 
- for_particle_neighbor(system, neighbor_system, coordinates, neighbor_coords,
- neighborhood_search;
- particles=eachparticle(system)) do particle,
- neighbor,
- pos_diff,
- distance
+ foreach_point_neighbor(system, neighbor_system, coordinates, neighbor_coords,
+ neighborhood_search;
+ points=eachparticle(system)) do particle, neighbor,
+ pos_diff, distance
  volume = hydrodynamic_mass(neighbor_system, neighbor) /
  particle_density(v_neighbor_system, neighbor_system, neighbor)
 

diff --git a/src/general/density_calculators.jl b/src/general/density_calculators.jl
@@ -62,8 +62,9 @@ function summation_density!(system, semi, u, u_ode, density;
  nhs = get_neighborhood_search(system, neighbor_system, semi)
 
  # Loop over all pairs of particles and neighbors within the kernel cutoff.
- for_particle_neighbor(system, neighbor_system, system_coords, neighbor_coords, nhs,
- particles=particles) do particle, neighbor, pos_diff, distance
+ foreach_point_neighbor(system, neighbor_system, system_coords, neighbor_coords, nhs,
+ points=particles) do particle, neighbor,
+ pos_diff, distance
  mass = hydrodynamic_mass(neighbor_system, neighbor)
  density[particle] += mass * smoothing_kernel(system, distance)
  end

diff --git a/src/general/initial_condition.jl b/src/general/initial_condition.jl
@@ -290,11 +290,12 @@ function find_too_close_particles(coords1, coords2, max_distance)
  NDIMS = size(coords1, 1)
  result = Int[]
 
- nhs = GridNeighborhoodSearch{NDIMS}(max_distance, size(coords2, 2))
+ nhs = GridNeighborhoodSearch{NDIMS}(search_radius=max_distance,
+ n_points=size(coords2, 2))
  PointNeighbors.initialize!(nhs, coords1, coords2)
 
  # We are modifying the vector `result`, so this cannot be parallel
- for_particle_neighbor(coords1, coords2, nhs, parallel=false) do particle, _, _, _
+ foreach_point_neighbor(coords1, coords2, nhs, parallel=false) do particle, _, _, _
  if !(particle in result)
  append!(result, particle)
  end

diff --git a/src/general/interpolation.jl b/src/general/interpolation.jl
@@ -495,7 +495,9 @@ function process_neighborhood_searches(semi, u_ode, ref_system, smoothing_length
  system_coords = current_coordinates(u, system)
  old_nhs = get_neighborhood_search(ref_system, system, semi)
  nhs = PointNeighbors.copy_neighborhood_search(old_nhs, search_radius,
- system_coords, system_coords)
+ nparticles(system))
+ PointNeighbors.initialize!(nhs, system_coords, system_coords)
+
  return nhs
  end
  end
@@ -534,7 +536,7 @@ end
 
  system_coords = current_coordinates(u, system)
 
- # This is basically `for_particle_neighbor` unrolled
+ # This is basically `foreach_point_neighbor` unrolled
  for particle in PointNeighbors.eachneighbor(point_coords, nhs)
  coords = extract_svector(system_coords, Val(ndims(system)), particle)
 

diff --git a/src/general/neighborhood_search.jl b/src/general/neighborhood_search.jl
@@ -1,22 +1,22 @@
 # Loop over all pairs of particles and neighbors within the kernel cutoff.
 # `f(particle, neighbor, pos_diff, distance)` is called for every particle-neighbor pair.
 # By default, loop over `each_moving_particle(system)`.
-function PointNeighbors.for_particle_neighbor(f, system, neighbor_system,
- system_coords, neighbor_coords,
- neighborhood_search;
- particles=each_moving_particle(system),
- parallel=true)
- for_particle_neighbor(f, system_coords, neighbor_coords, neighborhood_search,
- particles=particles, parallel=parallel)
+function PointNeighbors.foreach_point_neighbor(f, system, neighbor_system,
+  system_coords, neighbor_coords,
+  neighborhood_search;
+  points=each_moving_particle(system),
+  parallel=true)
+ foreach_point_neighbor(f, system_coords, neighbor_coords, neighborhood_search;
+  points, parallel)
 end
 
-function PointNeighbors.for_particle_neighbor(f, system::GPUSystem, neighbor_system,
- system_coords, neighbor_coords,
- neighborhood_search;
- particles=each_moving_particle(system),
- parallel=true)
- @threaded system for particle in particles
+function PointNeighbors.foreach_point_neighbor(f, system::GPUSystem, neighbor_system,
+  system_coords, neighbor_coords,
+  neighborhood_search;
+  points=each_moving_particle(system),
+  parallel=true)
+ @threaded system for point in points
  PointNeighbors.foreach_neighbor(f, system_coords, neighbor_coords,
- neighborhood_search, particle)
+ neighborhood_search, point)
  end
 end