Fix docstring-constructor mismatches, wrong variable references, and kinetic_energy double-counting

src/callbacks/density_reinit.jl

@@ -1,13 +1,14 @@
 """
-    DensityReinitializationCallback(; interval::Integer=0, dt=0.0)
+    DensityReinitializationCallback(particle_system; interval::Integer=0, dt=0.0,
+                                    reinit_initial_solution=true)
 
 Callback to reinitialize the density field when using [`ContinuityDensity`](@ref) [Panizzo2007](@cite).
 
 # Keywords
 - `interval=0`:              Reinitialize the density every `interval` time steps.
 - `dt`:                      Reinitialize the density in regular intervals of `dt` in terms
                              of integration time.
-- `reinit_initial_solution`: Reinitialize the initial solution (default=false)
+- `reinit_initial_solution`: Reinitialize the initial solution (default=true)
 """
 mutable struct DensityReinitializationCallback{I}
     interval::I

src/callbacks/post_process.jl

@@ -36,7 +36,7 @@ a fixed interval of simulation time (`dt`).
 - `output_directory="out"`: The path where the results of the post-processing will be saved.
 - `write_csv=true`: If set to `true`, write a csv file.
 - `write_json=true`: If set to `true`, write a json file.
-- `append_timestep=false`: If set to `true`, the current timestamp will be added to the filename.
+- `append_timestamp=false`: If set to `true`, the current timestamp will be added to the filename.
 - `write_file_interval=1`: Files will be written after every `write_file_interval` number of
                            postprocessing execution steps. A value of 0 indicates that files
                            are only written at the end of the simulation, eliminating I/O overhead.

src/general/corrections.jl

@@ -277,7 +277,7 @@ the correction matrix $\bm{L}_a$ is evaluated explicitly as
 struct GradientCorrection end
 
 @doc raw"""
-    BlendedGradientCorrection()
+    BlendedGradientCorrection(blending_factor)
 
 Calculate a blended gradient to reduce the stability issues of the [`GradientCorrection`](@ref)
 as explained by [Bonet (1999)](@cite Bonet1999).

src/general/custom_quantities.jl

@@ -22,11 +22,10 @@ function kinetic_energy(system::AbstractStructureSystem,
                         dv_ode, du_ode, v_ode, u_ode, semi, t)
     v = wrap_v(v_ode, system, semi)
     mass = system.mass
-    energy = zero(eltype(system))
 
     return sum(each_active_particle(system)) do particle
         v_i = current_velocity(v, system, particle)
-        energy += mass[particle] * dot(v_i, v_i) / 2
+        mass[particle] * dot(v_i, v_i) / 2
     end
 end
 

src/general/initial_condition.jl

@@ -436,7 +436,7 @@ end
 
 function move_particles_to_end!(ic::InitialCondition, particle_ids_to_move)
     invalid_id = findfirst(i -> i <= 0 || i > nparticles(ic), particle_ids_to_move)
-    isnothing(invalid_id) || throw(BoundsError(ic, invalid_id))
+    isnothing(invalid_id) || throw(BoundsError(ic, particle_ids_to_move[invalid_id]))
 
     sort_key = [i in particle_ids_to_move ? 1 : 0 for i in eachparticle(ic)]
     # Determine a permutation that sorts 'sort_key' in ascending order
@@ -453,7 +453,7 @@ end
 
 function move_particles_to_end!(a::AbstractVector, particle_ids_to_move)
     invalid_id = findfirst(i -> i <= 0 || i > length(a), particle_ids_to_move)
-    isnothing(invalid_id) || throw(BoundsError(a, invalid_id))
+    isnothing(invalid_id) || throw(BoundsError(a, particle_ids_to_move[invalid_id]))
 
     sort_key = [i in particle_ids_to_move ? 1 : 0 for i in eachindex(a)]
     # determine a permutation that sorts 'sort_key' in ascending order

src/general/interpolation.jl

@@ -420,7 +420,7 @@ The interpolation utilizes the same kernel function of the SPH simulation to wei
 contributions from nearby particles.
 
 See also: [`interpolate_line`](@ref), [`interpolate_plane_2d`](@ref),
-          [`interpolate_plane_2d_vtk`](@ref), [`interpolate_plane_3d`](@ref), .
+          [`interpolate_plane_2d_vtk`](@ref), [`interpolate_plane_3d`](@ref).
 
 # Arguments
 - `point_coords`:   A matrix of point coordinates, where the $i$-th column holds the

src/preprocessing/geometries/polygon.jl

@@ -107,7 +107,7 @@ function Base.show(io::IO, ::MIME"text/plain", geometry::Polygon)
     @nospecialize geometry # reduce precompilation time
 
     if get(io, :compact, false)
-        show(io, system)
+        show(io, geometry)
     else
         summary_header(io, "Polygon{$(ndims(geometry)), $(eltype(geometry))}")
         summary_line(io, "#edges", "$(nfaces(geometry))")

src/preprocessing/geometries/triangle_mesh.jl

@@ -156,7 +156,7 @@ function Base.show(io::IO, ::MIME"text/plain", geometry::TriangleMesh)
     @nospecialize geometry # reduce precompilation time
 
     if get(io, :compact, false)
-        show(io, system)
+        show(io, geometry)
     else
         summary_header(io, "TriangleMesh{$(ndims(geometry)), $(eltype(geometry))}")
         summary_line(io, "#faces", "$(nfaces(geometry))")

src/preprocessing/point_in_poly/winding_number_jacobson.jl

@@ -91,7 +91,7 @@ function Base.show(io::IO, ::MIME"text/plain", winding::WindingNumberJacobson)
     @nospecialize winding # reduce precompilation time
 
     if get(io, :compact, false)
-        show(io, system)
+        show(io, winding)
     else
         summary_header(io, "WindingNumberJacobson")
         summary_line(io, "winding number factor",

src/schemes/boundary/open_boundary/mirroring.jl

@@ -17,7 +17,7 @@ struct FirstOrderMirroring{ELTYPE}
 end
 
 """
-    SimpleMirroring(; firstorder_tolerance=1f-3))
+    SimpleMirroring(; firstorder_tolerance=1f-3)
 
 This method is similar to [`FirstOrderMirroring`](@ref), but does not use
 the corrected gradient as proposed by [Negi et al. (2022)](@cite Negi2022).

src/schemes/boundary/wall_boundary/dummy_particles.jl

@@ -120,7 +120,7 @@ struct AdamiPressureExtrapolation{ELTYPE}
 end
 
 @doc raw"""
-    BernoulliPressureExtrapolation(; pressure_offset=0, factor=1)
+    BernoulliPressureExtrapolation(; pressure_offset=0, factor=1, allow_loop_flipping=true)
 
 `density_calculator` for `BoundaryModelDummyParticles`.
 

src/schemes/fluid/entropically_damped_sph/system.jl

@@ -4,11 +4,13 @@
                                 pressure_acceleration=inter_particle_averaged_pressure,
                                 density_calculator=SummationDensity(),
                                 shifting_technique=nothing,
+                                average_pressure_reduction=(!isnothing(shifting_technique)),
                                 alpha=0.5, viscosity=nothing,
-                                acceleration=ntuple(_ -> 0.0, NDIMS), surface_tension=nothing,
+                                acceleration=ntuple(_ -> 0.0, NDIMS),
+                                correction=nothing,
+                                source_terms=nothing, surface_tension=nothing,
                                 surface_normal_method=nothing, buffer_size=nothing,
-                                reference_particle_spacing=0.0, color_value=1,
-                                source_terms=nothing)
+                                reference_particle_spacing=0.0, color_value=1)
 
 System for particles of a fluid.
 As opposed to the [weakly compressible SPH scheme](@ref wcsph), which uses an equation of state,

src/schemes/fluid/surface_tension.jl

@@ -2,7 +2,7 @@ abstract type AbstractSurfaceTension end
 abstract type AkinciTypeSurfaceTension <: AbstractSurfaceTension end
 
 @doc raw"""
-    CohesionForceAkinci(surface_tension_coefficient=1.0)
+    CohesionForceAkinci(; surface_tension_coefficient=1.0)
 
 This model only implements the cohesion force of the Akinci [Akinci2013](@cite) surface tension model.
 
@@ -21,7 +21,7 @@ struct CohesionForceAkinci{ELTYPE} <: AkinciTypeSurfaceTension
 end
 
 @doc raw"""
-    SurfaceTensionAkinci(surface_tension_coefficient=1.0)
+    SurfaceTensionAkinci(; surface_tension_coefficient=1.0)
 
 Implements a model for surface tension and adhesion effects drawing upon the
 principles outlined by Akinci [Akinci2013](@cite). This model is instrumental in capturing the nuanced
@@ -44,7 +44,7 @@ struct SurfaceTensionAkinci{ELTYPE} <: AkinciTypeSurfaceTension
 end
 
 @doc raw"""
-    SurfaceTensionMorris(surface_tension_coefficient=1.0)
+    SurfaceTensionMorris(; surface_tension_coefficient=1.0)
 
 This model implements the surface tension approach described by Morris [Morris2000](@cite).
 It calculates surface tension forces based on the curvature of the fluid interface
@@ -76,7 +76,7 @@ function create_cache_surface_tension(::SurfaceTensionMorris, ELTYPE, NDIMS, npa
 end
 
 @doc raw"""
-    SurfaceTensionMomentumMorris(surface_tension_coefficient=1.0)
+    SurfaceTensionMomentumMorris(; surface_tension_coefficient=1.0)
 
 This model implements the momentum-conserving surface tension approach outlined by Morris
 [Morris2000](@cite). It calculates surface tension forces using the divergence of a stress

src/schemes/fluid/weakly_compressible_sph/system.jl

@@ -9,7 +9,7 @@
                                 buffer_size=nothing,
                                 correction=nothing, source_terms=nothing,
                                 surface_tension=nothing, surface_normal_method=nothing,
-                                reference_particle_spacing=0.0, color_value=1))
+                                reference_particle_spacing=0.0, color_value=1)
 
 System for particles of a fluid.
 The weakly compressible SPH (WCSPH) scheme is used, wherein a stiff equation of state

src/schemes/structure/discrete_element_method/system.jl

@@ -132,13 +132,13 @@ initialize!(system::DEMSystem, semi) = system
 
 function compact_support(system::DEMSystem, neighbor::DEMSystem)
     # we for now assume that the compact support is 3 * radius
-    # todo: needs to be changed for more complex simulations
+    # TODO: needs to be changed for more complex simulations
     return 3 * max(maximum(system.radius), maximum(neighbor.radius))
 end
 
 function compact_support(system::DEMSystem, neighbor)
     # we for now assume that the compact support is 3 * radius
-    # todo: needs to be changed for more complex simulations
+    # TODO: needs to be changed for more complex simulations
     return 3 * maximum(system.radius)
 end
 

src/setups/complex_shape.jl

@@ -2,7 +2,7 @@
     ComplexShape(geometry::Union{TriangleMesh, Polygon}; particle_spacing, density,
                  pressure=0.0, mass=nothing, velocity=zeros(ndims(geometry)),
                  point_in_geometry_algorithm=WindingNumberJacobson(; geometry,
-                                                                   hierarchical_winding=false,
+                                                                   hierarchical_winding=true,
                                                                    winding_number_factor=sqrt(eps())),
                  grid_offset::Real=0.0, max_nparticles=10^7,
                  pad_initial_particle_grid=2particle_spacing)

src/setups/extrude_geometry.jl

@@ -1,6 +1,6 @@
 @doc raw"""
     extrude_geometry(geometry; particle_spacing, direction, n_extrude::Integer,
-                     velocity=zeros(length(direction)),
+                     velocity=zeros(length(direction)), place_on_shell=false,
                      mass=nothing, density=nothing, pressure=0.0)
 
 Extrude either a line, a plane or a shape along a specific direction.