Generalize surface normal calc #539

svchb · 2024-05-29T10:49:04Z

Depends on #599
extracted from #584

Conflicts: src/schemes/fluid/weakly_compressible_sph/system.jl

…vchb/TrixiParticles.jlOpen into generalize_surface_normal_calc

Conflicts: examples/fluid/dam_break_oil_film_2d.jl src/schemes/fluid/weakly_compressible_sph/state_equations.jl

NEWS.md

src/schemes/boundary/dummy_particles/dummy_particles.jl

src/schemes/fluid/surface_normal_sph.jl

src/schemes/fluid/entropically_damped_sph/system.jl

…vchb/TrixiParticles.jlOpen into generalize_surface_normal_calc

docs/src/systems/fluid.md

efaulhaber · 2024-12-03T08:06:35Z

src/schemes/fluid/weakly_compressible_sph/system.jl

    initial_condition                 :: IC
    mass                              :: MA     # Array{ELTYPE, 1}
    pressure                          :: P      # Array{ELTYPE, 1}
    density_calculator                :: DC
    state_equation                    :: SE
    smoothing_kernel                  :: K
    smoothing_length                  :: ELTYPE
+    ideal_neighbor_count              :: Int
+    color                             :: Int


This is never used, is it? Same for EDAC.

Yes it will be used in #584

As always, please remove it from this PR and add it when it's actually used.

test/schemes/fluid/surface_normal_sph.jl

efaulhaber · 2024-12-03T08:50:38Z

test/schemes/fluid/surface_normal_sph.jl

+
+    # After computation, check that surface normals have been computed
+    @test all(isfinite.(system.cache.surface_normal))
+    @test all(isfinite.(system.cache.neighbor_count))


Isn't this zero by default? Shouldn't you then check that this is not zero anymore?

The inside will stay at 0.0. though.

test/schemes/fluid/surface_normal_sph.jl

efaulhaber · 2024-12-03T09:09:38Z

test/schemes/fluid/surface_normal_sph.jl

+    for i in surface_particles
+        @test isapprox(computed_normals[:, i], expected_normals[:, i], atol=0.05)
+    end


Suggested change

for i in surface_particles

@test isapprox(computed_normals[:, i], expected_normals[:, i], atol=0.05)

end

@test isapprox(computed_normals, expected_normals, atol=0.05)

The loop will generate a lot of tests.

This doesn't work since the normals are not always exactly 0.0 on the inside.

@test isapprox(computed_normals[:, surface_particles], expected_normals[:, surface_particles], atol=0.05)

efaulhaber · 2024-12-03T09:09:43Z

test/schemes/fluid/surface_normal_sph.jl

+    # Optionally, check that normals for interior particles are zero
+    # for i in setdiff(1:nparticles, surface_particles)
+    #     @test isapprox(norm(system.cache.surface_normal[:, i]), 0.0, atol=1e-4)
+    # end


This is also part of #584

I thought I used it there but this is rather tricky... Even with the special conditions that are implemented in #584

And with a larger tolerance? There should be some test to ensure the inner values are not completely random.
And there should not be a commented out test in here.

…vchb/TrixiParticles.jlOpen into generalize_surface_normal_calc

efaulhaber · 2024-12-09T07:56:51Z

test/schemes/fluid/surface_normal_sph.jl

@@ -96,18 +84,18 @@ end
    center = (0.0, 0.0)
    NDIMS = 2

-    # Create a SphereShape (which is a circle in 2D)
+    # Create a `SphereShape`, which is a circle in 2D


A circle is the surface, a disk is a filled circle.

efaulhaber · 2024-12-09T07:59:00Z

test/schemes/fluid/surface_normal_sph.jl

+    for i in surface_particles
+        @test isapprox(computed_normals[:, i], expected_normals[:, i], atol=0.05)
+    end


@test isapprox(computed_normals[:, surface_particles], expected_normals[:, surface_particles], atol=0.05)

efaulhaber · 2024-12-09T08:01:37Z

Project.toml

@@ -1,7 +1,7 @@
 name = "TrixiParticles"
 uuid = "66699cd8-9c01-4e9d-a059-b96c86d16b3a"
 authors = ["erik.faulhaber <[email protected]>"]
-version = "0.2.4-dev"
+version = "0.2.4"


I think it makes more sense to wait for #529 before we release.

efaulhaber · 2024-12-09T08:13:31Z

src/schemes/fluid/surface_normal_sph.jl

+    foreach_point_neighbor(system, neighbor_system,
+                           system_coords, neighbor_system_coords,
+                           nhs) do particle, neighbor, pos_diff, distance
+        colorfield[neighbor] += smoothing_kernel(system, distance)
+    end


Suggested change

foreach_point_neighbor(system, neighbor_system,

system_coords, neighbor_system_coords,

nhs) do particle, neighbor, pos_diff, distance

colorfield[neighbor] += smoothing_kernel(system, distance)

end

foreach_point_neighbor(neighbor_system, system,

neighbor_system_coords, system_coords,

nhs) do particle, neighbor, pos_diff, distance

colorfield[particle] += smoothing_kernel(system, distance)

end

Otherwise you will get race conditions on multiple threads.

efaulhaber · 2024-12-09T08:14:00Z

src/schemes/fluid/surface_normal_sph.jl

+    end
+
+    @threaded neighbor_system for bnd_particle in eachparticle(neighbor_system)
+        colorfield[bnd_particle] = colorfield[bnd_particle] / (colorfield[bnd_particle] +


Why is colorfield_bnd initialized elsewhere and not here where colorfield is computed?

efaulhaber · 2024-12-09T08:16:14Z

test/schemes/fluid/surface_normal_sph.jl

+
+    nparticles = size(u, 2)
+
+    # check the threshold has been applied correctly


Suggested change

# check the threshold has been applied correctly

# Check that the threshold has been applied correctly

#133

efaulhaber · 2024-12-09T08:16:45Z

test/schemes/fluid/surface_normal_sph.jl

+        if system.cache.neighbor_count[i] < threshold
+            @test all(system.cache.surface_normal[:, i] .== 0.0)
+        else
+            # For the linear arrangement, surface normals may still be zero
+            # Adjust the test to account for this possibility
+            @test true
+        end


Can you please fix this here then?

efaulhaber · 2024-12-09T08:18:21Z

src/schemes/fluid/fluid.jl

+@inline function surface_normal_method(system::FluidSystem)
+    return system.surface_normal_method
+end
+
+@inline function surface_normal_method(system)
+    return nothing
+end


Never used.

efaulhaber · 2024-12-09T08:19:03Z

src/schemes/boundary/system.jl

+function initialize_colorfield!(system, ::BoundaryModelDummyParticles, neighborhood_search)
+    system_coords = system.coordinates
+    (; smoothing_kernel, smoothing_length) = system.boundary_model
+
+    foreach_point_neighbor(system, system,
+                           system_coords, system_coords,
+                           neighborhood_search,
+                           points=eachparticle(system)) do particle, neighbor, pos_diff,
+                                                           distance
+        system.boundary_model.cache.colorfield_bnd[particle] += kernel(smoothing_kernel,
+                                                                       distance,
+                                                                       smoothing_length)
+        system.boundary_model.cache.neighbor_count[particle] += 1
+    end
+    return system
+end


Please add a test.

efaulhaber · 2024-12-09T08:21:59Z

src/general/system.jl

+    return floor(Int, pi * compact_support^2 / particle_spacing^2)
+end
+
+@inline @fastpow function ideal_neighbor_count(::Val{3}, particle_spacing, compact_support)


Please check the codecov report. This is not covered, but the 2D version is.

efaulhaber · 2024-12-09T08:24:06Z

src/schemes/fluid/surface_normal_sph.jl

+# Section 2.2 in Akinci et al. 2013 "Versatile Surface Tension and Adhesion for SPH Fluids"
+# Note: This is the simplest form of normal approximation commonly used in SPH and comes
+# with serious deficits in accuracy especially at corners, small neighborhoods and boundaries
+function calc_normal_akinci!(system, neighbor_system::BoundarySystem, u_system, v,


Please check Codecov report. This is missing tests.

svchb added 30 commits September 6, 2023 01:01

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…vchb/TrixiParticles.jlOpen into generalize_surface_normal_calc

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Conflicts: examples/fluid/dam_break_oil_film_2d.jl src/schemes/fluid/weakly_compressible_sph/state_equations.jl

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efaulhaber mentioned this pull request Nov 25, 2024

Move fields that are only sometimes needed to the cache? #676

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Generalize surface normal calc #539

Generalize surface normal calc #539

svchb commented May 29, 2024 •

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		nparticles = size(u, 2)

		# check the threshold has been applied correctly

	# check the threshold has been applied correctly
	# Check that the threshold has been applied correctly

Generalize surface normal calc #539

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Generalize surface normal calc #539

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svchb commented May 29, 2024 •

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