Refactor SPH system initialization to use keyword arguments

docs/literate/src/tut_custom_kernel.jl

@@ -117,13 +117,13 @@ nothing # hide
 # `examples/fluid/dam_break_2d.jl` with our custom kernel and the corresponding
 # smoothing length.
 # ```@cast @__NAME__; width=100, height=50, delay=0, loop=true, loop_delay=5
-# trixi_include(@__MODULE__, joinpath(examples_dir(), "fluid", "dam_break_2d.jl"),
+# trixi_include(@__MODULE__, joinpath(examples_dir(), "fluid", "dam_break_2d.jl");
 #               smoothing_kernel=MyGaussianKernel(),
-#               smoothing_length=smoothing_length);
+#               smoothing_length);
 # ```
-trixi_include(joinpath(examples_dir(), "fluid", "dam_break_2d.jl"), #!md
+trixi_include(joinpath(examples_dir(), "fluid", "dam_break_2d.jl"); #!md
               smoothing_kernel=MyGaussianKernel(), #!md
-              smoothing_length=smoothing_length) #!md
+              smoothing_length) #!md
 
 # See [Visualization](@ref) for how to visualize the final solution.
 # For the simplest visualization, we can use [Plots.jl](https://docs.juliaplots.org/stable/):

docs/literate/src/tut_packing.jl

@@ -49,7 +49,7 @@ signed_distance_field = SignedDistanceField(geometry, particle_spacing;
 # We can also visualize the SDF by simply creating an `InitialCondition` from the sampled points and plot it.
 # The color coding represents the signed distance to the geometry surface.
 sdf_ic = InitialCondition(; coordinates=stack(signed_distance_field.positions),
-                          density=1.0, particle_spacing=particle_spacing)
+                          density=1.0, particle_spacing)
 
 plot(sdf_ic, zcolor=signed_distance_field.distances, label=nothing, color=:coolwarm)
 plot!(geometry, linestyle=:dash, label=nothing, showaxis=false, color=:black,
@@ -64,7 +64,7 @@ signed_distance_field = SignedDistanceField(geometry, particle_spacing;
 
 # We can see in the plot that the SDF has been extended outwards to twice `max_signed_distance`.
 sdf_ic = InitialCondition(; coordinates=stack(signed_distance_field.positions),
-                          density=1.0, particle_spacing=particle_spacing)
+                          density=1.0, particle_spacing)
 
 plot(sdf_ic, zcolor=signed_distance_field.distances, label=nothing, color=:coolwarm)
 
@@ -105,7 +105,7 @@ point_in_geometry_algorithm = WindingNumberJacobson(; geometry)
 # This function creates an [`InitialCondition`](@ref InitialCondition) for the interior particles.
 # Here, we need to specify `particle_spacing` and `density`. For further arguments, please refer to
 # the documentation of [ComplexShape](@ref ComplexShape) or [InitialCondition](@ref InitialCondition).
-shape_sampled = ComplexShape(geometry; particle_spacing, density=density,
+shape_sampled = ComplexShape(geometry; particle_spacing, density,
                              point_in_geometry_algorithm)
 
 # If we want to assign the mass of each sampled particle consistently with its density,
@@ -147,8 +147,8 @@ smoothing_length = 0.8 * particle_spacing
 # Now we can create the packing system. For learning purposes, let’s first try
 # passing no signed distance field (SDF) and see what happens.
 packing_system = ParticlePackingSystem(shape_sampled;
-                                       smoothing_kernel=smoothing_kernel,
-                                       smoothing_length=smoothing_length,
+                                       smoothing_kernel,
+                                       smoothing_length,
                                        signed_distance_field=nothing, background_pressure)
 
 # We now proceed with the familiar steps
@@ -164,7 +164,7 @@ callbacks = CallbackSet(UpdateCallback())
 time_integrator = RDPK3SpFSAL35()
 
 sol = solve(ode, time_integrator;
-            abstol=1e-7, reltol=1e-4, save_everystep=false, maxiters=maxiters,
+            abstol=1e-7, reltol=1e-4, save_everystep=false, maxiters,
             callback=callbacks)
 
 packed_ic = InitialCondition(sol, packing_system, semi)
@@ -177,8 +177,8 @@ plot!(geometry, seriestype=:path, linewidth=2, color=:black, label=nothing)
 
 # We therefore add an SDF for the geometry and repeat the same procedure.
 packing_system = ParticlePackingSystem(shape_sampled;
-                                       smoothing_kernel=smoothing_kernel,
-                                       smoothing_length=smoothing_length,
+                                       smoothing_kernel,
+                                       smoothing_length,
                                        signed_distance_field,
                                        background_pressure)
 
@@ -193,7 +193,7 @@ callbacks = CallbackSet(UpdateCallback())
 time_integrator = RDPK3SpFSAL35()
 
 sol = solve(ode, time_integrator;
-            abstol=1e-7, reltol=1e-4, save_everystep=false, maxiters=maxiters,
+            abstol=1e-7, reltol=1e-4, save_everystep=false, maxiters,
             callback=callbacks)
 
 packed_ic = InitialCondition(sol, packing_system, semi)
@@ -216,8 +216,8 @@ plot!(geometry, seriestype=:path, color=:black, label=nothing, linewidth=2)
 # geometry size in this example, we will choose `0.7`.
 boundary_system = ParticlePackingSystem(boundary_sampled;
                                         is_boundary=true,
-                                        smoothing_kernel=smoothing_kernel,
-                                        smoothing_length=smoothing_length,
+                                        smoothing_kernel,
+                                        smoothing_length,
                                         boundary_compress_factor=0.7,
                                         signed_distance_field, background_pressure)
 
@@ -232,7 +232,7 @@ callbacks = CallbackSet(UpdateCallback())
 time_integrator = RDPK3SpFSAL35()
 
 sol = solve(ode, time_integrator;
-            abstol=1e-7, reltol=1e-4, save_everystep=false, maxiters=maxiters,
+            abstol=1e-7, reltol=1e-4, save_everystep=false, maxiters,
             callback=callbacks)
 
 packed_ic = InitialCondition(sol, packing_system, semi)
@@ -255,8 +255,8 @@ plot!(geometry, seriestype=:path, color=:black, linestyle=:dash, linewidth=2, la
 # Therefore, we set `fixed_system=true` so that this system is not integrated further
 # but instead serves as a static boundary for the packing of other domains.
 fixed_system = ParticlePackingSystem(packed_ic;
-                                     smoothing_kernel=smoothing_kernel,
-                                     smoothing_length=smoothing_length,
+                                     smoothing_kernel,
+                                     smoothing_length,
                                      signed_distance_field=nothing,
                                      background_pressure,
                                      fixed_system=true)
@@ -274,8 +274,8 @@ plot(sampled_outer_domain, packed_ic)
 
 # Next, we create a packing system for the outer domain.
 packing_system = ParticlePackingSystem(sampled_outer_domain;
-                                       smoothing_kernel=smoothing_kernel,
-                                       smoothing_length=smoothing_length,
+                                       smoothing_kernel,
+                                       smoothing_length,
                                        signed_distance_field=nothing,
                                        background_pressure)
 
@@ -294,7 +294,7 @@ callbacks = CallbackSet(UpdateCallback())
 time_integrator = RDPK3SpFSAL35()
 
 sol_1 = solve(ode, time_integrator; abstol=1e-7, reltol=1e-4,
-              save_everystep=false, maxiters=maxiters, callback=callbacks)
+              save_everystep=false, maxiters, callback=callbacks)
 
 packed_outer_domain = InitialCondition(sol_1, packing_system, semi)
 
@@ -324,21 +324,21 @@ plot(pack_domain, fixed_domain, packed_ic)
 # We can now treat the particles outside the window, along with the already
 # finalized configuration of the complex geometry, as fixed systems:
 fixed_system_1 = ParticlePackingSystem(fixed_domain;
-                                       smoothing_kernel=smoothing_kernel,
-                                       smoothing_length=smoothing_length,
+                                       smoothing_kernel,
+                                       smoothing_length,
                                        signed_distance_field=nothing,
                                        background_pressure, fixed_system=true)
 
 fixed_system_2 = ParticlePackingSystem(packed_ic;
-                                       smoothing_kernel=smoothing_kernel,
-                                       smoothing_length=smoothing_length,
+                                       smoothing_kernel,
+                                       smoothing_length,
                                        signed_distance_field=nothing,
                                        background_pressure, fixed_system=true)
 
 # The window that we want to pack is passed to a moving packing system:
 packing_system = ParticlePackingSystem(pack_domain;
-                                       smoothing_kernel=smoothing_kernel,
-                                       smoothing_length=smoothing_length,
+                                       smoothing_kernel,
+                                       smoothing_length,
                                        signed_distance_field=nothing,
                                        background_pressure)
 
@@ -352,7 +352,7 @@ callbacks = CallbackSet(UpdateCallback())
 time_integrator = RDPK3SpFSAL35()
 
 sol_2 = solve(ode, time_integrator; abstol=1e-7, reltol=1e-4,
-              save_everystep=false, maxiters=maxiters, callback=callbacks)
+              save_everystep=false, maxiters, callback=callbacks)
 
 packed_fluid_domain = InitialCondition(sol_2, packing_system, semi)
 

docs/literate/src/tut_rigid_body_fsi.jl

@@ -42,10 +42,10 @@ sound_speed = 100.0
 state_equation = StateEquationCole(; sound_speed, reference_density=fluid_density,
                                    exponent=1)
 
-tank = RectangularTank(fluid_particle_spacing, initial_fluid_size, tank_size, fluid_density,
-                       n_layers=boundary_layers, spacing_ratio=spacing_ratio,
+tank = RectangularTank(fluid_particle_spacing, initial_fluid_size, tank_size, fluid_density;
+                       n_layers=boundary_layers, spacing_ratio,
                        faces=(true, true, true, false),
-                       acceleration=(0.0, -gravity), state_equation=state_equation)
+                       acceleration=(0.0, -gravity), state_equation)
 nothing # hide
 
 # ## Rigid body geometry
@@ -97,10 +97,13 @@ fluid_density_calculator = ContinuityDensity()
 viscosity = ArtificialViscosityMonaghan(alpha=0.02, beta=0.0)
 density_diffusion = DensityDiffusionMolteniColagrossi(delta=0.1)
 
-fluid_system = WeaklyCompressibleSPHSystem(tank.fluid, fluid_density_calculator,
-                                           state_equation, fluid_smoothing_kernel,
-                                           fluid_smoothing_length, viscosity=viscosity,
-                                           density_diffusion=density_diffusion,
+fluid_system = WeaklyCompressibleSPHSystem(tank.fluid;
+                                           smoothing_kernel=fluid_smoothing_kernel,
+                                           smoothing_length=fluid_smoothing_length,
+                                           density_calculator=fluid_density_calculator,
+                                           state_equation,
+                                           viscosity,
+                                           density_diffusion,
                                            acceleration=(0.0, -gravity))
 nothing # hide
 
@@ -166,10 +169,10 @@ nothing # hide
 boundary_density_calculator = AdamiPressureExtrapolation()
 tank_boundary_model = BoundaryModelDummyParticles(tank.boundary.density,
                                                   tank.boundary.mass,
-                                                  state_equation=state_equation,
                                                   boundary_density_calculator,
                                                   fluid_smoothing_kernel,
-                                                  fluid_smoothing_length)
+                                                  fluid_smoothing_length;
+                                                  state_equation)
 
 boundary_system = WallBoundarySystem(tank.boundary, tank_boundary_model)
 nothing # hide
@@ -180,10 +183,10 @@ function rigid_body_boundary_model(shape)
                           structure_particle_spacing^ndims(fluid_system)
 
     return BoundaryModelDummyParticles(hydrodynamic_densities, hydrodynamic_masses,
-                                       state_equation=state_equation,
                                        boundary_density_calculator,
                                        fluid_smoothing_kernel,
-                                       fluid_smoothing_length)
+                                       fluid_smoothing_length;
+                                       state_equation)
 end
 
 square1_boundary_model = rigid_body_boundary_model(square1)
@@ -236,12 +239,12 @@ nothing # hide
 
 rigid_body_system_1_step3 = RigidBodySystem(square1;
                                             boundary_model=square1_boundary_model,
-                                            contact_model=contact_model,
+                                            contact_model,
                                             acceleration=(0.0, -gravity),
                                             particle_spacing=structure_particle_spacing)
 rigid_body_system_2_step3 = RigidBodySystem(square2;
                                             boundary_model=square2_boundary_model,
-                                            contact_model=contact_model,
+                                            contact_model,
                                             acceleration=(0.0, -gravity),
                                             particle_spacing=structure_particle_spacing)
 nothing # hide
@@ -303,12 +306,12 @@ nothing # hide
 
 rigid_body_system_1_step4 = RigidBodySystem(circle1;
                                             boundary_model=circle1_boundary_model,
-                                            contact_model=contact_model,
+                                            contact_model,
                                             acceleration=(0.0, -gravity),
                                             particle_spacing=structure_particle_spacing)
 rigid_body_system_2_step4 = RigidBodySystem(circle2;
                                             boundary_model=circle2_boundary_model,
-                                            contact_model=contact_model,
+                                            contact_model,
                                             acceleration=(0.0, -gravity),
                                             particle_spacing=structure_particle_spacing)
 nothing # hide
@@ -361,7 +364,7 @@ small_sphere_systems = [begin
                             sphere_boundary_model = rigid_body_boundary_model(sphere)
                             RigidBodySystem(sphere;
                                             boundary_model=sphere_boundary_model,
-                                            contact_model=contact_model,
+                                            contact_model,
                                             acceleration=(0.0, -gravity),
                                             particle_spacing=structure_particle_spacing)
                         end
@@ -420,7 +423,7 @@ hexagon_boundary_model = rigid_body_boundary_model(hexagon_shape)
 
 hexagon_system = RigidBodySystem(hexagon_shape;
                                  boundary_model=hexagon_boundary_model,
-                                 contact_model=contact_model,
+                                 contact_model,
                                  acceleration=(0.0, -gravity),
                                  particle_spacing=structure_particle_spacing)
 #

docs/literate/src/tut_setup.jl

@@ -80,8 +80,8 @@ nothing # hide
 # fluid inside a rectangular tank, and supports a hydrostatic pressure gradient
 # by passing a gravitational acceleration and a state equation (see above).
 tank = RectangularTank(fluid_particle_spacing, initial_fluid_size, tank_size,
-                       fluid_density, n_layers=boundary_layers,
-                       acceleration=(0.0, -gravity), state_equation=state_equation)
+                       fluid_density; n_layers=boundary_layers,
+                       acceleration=(0.0, -gravity), state_equation)
 nothing # hide
 # A `RectangularTank` consists of two [`InitialCondition`](@ref)s, `tank.fluid` and `tank.boundary`.
 # We can plot these initial conditions to visualize the initial setup.
@@ -120,10 +120,12 @@ nothing # hide
 # The simulation quality greatly benefits from using [density diffusion](@ref density_diffusion).
 fluid_density_calculator = ContinuityDensity()
 density_diffusion = DensityDiffusionMolteniColagrossi(delta=0.1)
-fluid_system = WeaklyCompressibleSPHSystem(tank.fluid, fluid_density_calculator,
-                                           state_equation, smoothing_kernel,
-                                           smoothing_length, viscosity=viscosity,
-                                           density_diffusion=density_diffusion,
+fluid_system = WeaklyCompressibleSPHSystem(tank.fluid;
+                                           smoothing_kernel, smoothing_length,
+                                           density_calculator=fluid_density_calculator,
+                                           state_equation,
+                                           viscosity,
+                                           density_diffusion,
                                            acceleration=(0.0, -gravity))
 nothing # hide
 
@@ -136,9 +138,9 @@ nothing # hide
 # We will use the [`BoundaryModelDummyParticles`](@ref) with [`AdamiPressureExtrapolation`](@ref).
 # See [here](@ref boundary_models) for a comprehensive overview over boundary models.
 boundary_model = BoundaryModelDummyParticles(tank.boundary.density, tank.boundary.mass,
-                                             state_equation=state_equation,
                                              AdamiPressureExtrapolation(),
-                                             smoothing_kernel, smoothing_length)
+                                             smoothing_kernel, smoothing_length;
+                                             state_equation)
 boundary_system = WallBoundarySystem(tank.boundary, boundary_model)
 nothing # hide
 

examples/dem/collapsing_sand_pile_3d.jl

@@ -64,12 +64,12 @@ boundary_particles = floor_particles
 contact_model = LinearContactModel(1e6)
 damping_coefficient = 0.00001
 
-sand_system = DEMSystem(sand_particles, contact_model;
-                        damping_coefficient=damping_coefficient,
-                        acceleration=acceleration, radius=0.4 * particle_spacing)
+sand_system = DEMSystem(sand_particles; contact_model,
+                        damping_coefficient,
+                        acceleration, radius=0.4 * particle_spacing)
 
 boundary_stiffness = 1.0e5
-boundary_system = BoundaryDEMSystem(boundary_particles, boundary_stiffness)
+boundary_system = BoundaryDEMSystem(boundary_particles; normal_stiffness=boundary_stiffness)
 
 # ==========================================================================================
 # ==== Simulation

examples/dem/rectangular_tank_2d.jl

@@ -47,11 +47,11 @@ contact_model = HertzContactModel(10e9, 0.3)
 # contact_model = LinearContactModel(2 * 10e5)
 
 # Construct the rock system using the new DEMSystem signature.
-rock_system = DEMSystem(tank.fluid, contact_model; damping_coefficient=0.0001,
+rock_system = DEMSystem(tank.fluid; contact_model, damping_coefficient=0.0001,
                         acceleration=(0.0, gravity), radius=0.4 * particle_spacing)
 
 # Construct the boundary system for the tank walls.
-boundary_system = BoundaryDEMSystem(tank.boundary, 10e7)
+boundary_system = BoundaryDEMSystem(tank.boundary; normal_stiffness=10e7)
 
 # ==========================================================================================
 # ==== Simulation