Merge branch 'main' into validate-open-boundaries

LasNikas · LasNikas · commit ee61bc89697c · 2025-10-22T19:44:32.000+02:00
diff --git a/Project.toml b/Project.toml
@@ -50,7 +50,7 @@ FastPow = "0.1"
 FileIO = "1"
 ForwardDiff = "1"
 GPUArraysCore = "0.2"
-JSON = "0.21"
+JSON = "1"
 KernelAbstractions = "0.9"
 MuladdMacro = "0.2"
 OrdinaryDiffEq = "6.91"
diff --git a/docs/literate/src/tut_packing.jl b/docs/literate/src/tut_packing.jl
@@ -140,7 +140,7 @@ background_pressure = 1.0
 
 # For particle interaction, we select a [smoothing kernel](@ref smoothing_kernel)
 # with a suitable smoothing length. Empirically, a factor of `0.8` times the
-# particle spacing gives good results [Neher2025](@cite).
+# particle spacing gives good results [Neher2026](@cite).
 smoothing_kernel = SchoenbergQuinticSplineKernel{2}()
 smoothing_length = 0.8 * particle_spacing
 
@@ -203,7 +203,7 @@ plot(packed_ic)
 plot!(geometry, seriestype=:path, color=:black, label=nothing, linewidth=2)
 
 # We can see that the particles now stay inside the geometry,
-# but their distribution near the surface can still be improved by adding boundary particles [Neher2025](@cite).
+# but their distribution near the surface can still be improved by adding boundary particles [Neher2026](@cite).
 # Therefore, we set up a dedicated boundary packing system
 # by setting `is_boundary = true`.
 # For convex geometries, it is useful to slightly compress the
diff --git a/docs/src/preprocessing/preprocessing.md b/docs/src/preprocessing/preprocessing.md
@@ -302,7 +302,7 @@ Pages = [joinpath("preprocessing", "geometries", "io.jl")]
 ```
 
 # [Particle Packing](@id particle_packing)
-To obtain a body-fitted and isotropic particle distribution, an initial configuration (see [Sampling of Geometries](@ref sampling_of_geometries)) is first generated. This configuration is then packed using a [`ParticlePackingSystem`](@ref) following the steps introduced in [Neher2025](@cite).
+To obtain a body-fitted and isotropic particle distribution, an initial configuration (see [Sampling of Geometries](@ref sampling_of_geometries)) is first generated. This configuration is then packed using a [`ParticlePackingSystem`](@ref) following the steps introduced in [Neher2026](@cite).
 For a hands-on tutorial with complete examples, see the particle packing tutorial.
 The preprocessing pipeline consists of the following steps:
 
diff --git a/docs/src/refs.bib b/docs/src/refs.bib
@@ -636,14 +636,14 @@ @Article{Negi2022
   publisher = {{AIP} Publishing},
 }
 
-@Misc{Neher2025,
-  author        = {Neher, Niklas S. and Faulhaber, Erik and Berger, Sven and Wei{\ss}enfels, Christian and Gassner, Gregor J. and Schlottke-Lakemper, Michael},
-  title         = {Robust and efficient pre-processing techniques for particle-based methods including dynamic boundary generation},
-  month         = jun,
-  year          = {2025},
-  archiveprefix = {arXiv},
-  eprint        = {2506.12106},
-  primaryclass  = {math.NA},
+@Article{Neher2026,
+  author    = {Neher, Niklas S. and Faulhaber, Erik and Berger, Sven and Wei{\ss}enfels, Christian and Gassner, Gregor J. and Schlottke-Lakemper, Michael},
+  journal   = {Computer Physics Communications},
+  title     = {Robust and efficient pre-processing techniques for particle-based methods including dynamic boundary generation},
+  year      = {2026},
+  pages     = {109898},
+  volume    = {318},
+  doi       = {10.1016/j.cpc.2025.109898}
 }
 
 @Article{OConnor2021,
diff --git a/test/Project.toml b/test/Project.toml
@@ -17,11 +17,11 @@ TrixiTest = "0a316866-cbd0-4425-8bcb-08103b2c1f26"
 
 [compat]
 CSV = "0.10"
-CairoMakie = "0.13, 0.15"
+CairoMakie = "0.15"
 DataFrames = "1.6"
 GLM = "1.9"
 Glob = "1.3"
-JSON = "0.21"
+JSON = "1"
 OrdinaryDiffEq = "6.49"
 Plots = "1"
 Polyester = "0.7"
diff --git a/test/systems/iisph_system.jl b/test/systems/iisph_system.jl
@@ -253,7 +253,7 @@
                                                  time_step=0.001)
 
         u0 = zeros(TrixiParticles.u_nvariables(system),
-                   TrixiParticles.n_moving_particles(system))
+                   TrixiParticles.n_integrated_particles(system))
         TrixiParticles.write_u0!(u0, system)
 
         @test u0 == coordinates
@@ -279,7 +279,7 @@
                                                  time_step=0.001)
 
         v0 = zeros(TrixiParticles.v_nvariables(system),
-                   TrixiParticles.n_moving_particles(system))
+                   TrixiParticles.n_integrated_particles(system))
         TrixiParticles.write_v0!(v0, system)
 
         @test v0 == velocity
diff --git a/test/systems/systems.jl b/test/systems/systems.jl
@@ -5,3 +5,4 @@ include("boundary_system.jl")
 include("open_boundary_system.jl")
 include("dem_system.jl")
 include("packing_system.jl")
+include("iisph_system.jl")
