Updated sigma

Manifest.toml

@@ -73,9 +73,9 @@ version = "1.2.2"
 
 [[deps.BitTwiddlingConvenienceFunctions]]
 deps = ["Static"]
-git-tree-sha1 = "bc1317f71de8dce26ea67fcdf7eccc0d0693b75b"
+git-tree-sha1 = "5e98d6a6aa92e5758c4d58501b7bf23732699fa3"
 uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b"
-version = "0.1.1"
+version = "0.1.2"
 
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -90,9 +90,9 @@ version = "0.4.1"
 
 [[deps.CPUSummary]]
 deps = ["Hwloc", "IfElse", "Static"]
-git-tree-sha1 = "87b0c9c6ee0124d6c1f4ce8cb035dcaf9f90b803"
+git-tree-sha1 = "ba19d1c8ff6b9c680015033c66802dd817a9cf39"
 uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
-version = "0.1.6"
+version = "0.1.7"
 
 [[deps.CSV]]
 deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"]
@@ -126,15 +126,15 @@ version = "1.16.1+1"
 
 [[deps.CellListMap]]
 deps = ["DocStringExtensions", "LinearAlgebra", "Parameters", "ProgressMeter", "Random", "Setfield", "StaticArrays"]
-git-tree-sha1 = "8450164cabc2a60e4352a7d2350fe528c18e0315"
+git-tree-sha1 = "a8bbe24072214a78629ef5a44593bb886be37a1a"
 uuid = "69e1c6dd-3888-40e6-b3c8-31ac5f578864"
-version = "0.7.1"
+version = "0.7.2"
 
 [[deps.ChainRules]]
 deps = ["ChainRulesCore", "Compat", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "Statistics"]
-git-tree-sha1 = "e659ddd9b3d67b236c750805e0176217f26d70a9"
+git-tree-sha1 = "3ce62c97bd166b8c810889fba131531c61e41dc8"
 uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
-version = "1.23.0"
+version = "1.25.0"
 
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
@@ -545,9 +545,9 @@ version = "2.8.1+1"
 
 [[deps.HostCPUFeatures]]
 deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"]
-git-tree-sha1 = "8f0dc80088981ab55702b04bba38097a44a1a3a9"
+git-tree-sha1 = "3965a3216446a6b020f0d48f1ba94ef9ec01720d"
 uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0"
-version = "0.1.5"
+version = "0.1.6"
 
 [[deps.Hwloc]]
 deps = ["Hwloc_jll"]
@@ -668,9 +668,9 @@ version = "1.0.0"
 
 [[deps.JLD2]]
 deps = ["DataStructures", "FileIO", "MacroTools", "Mmap", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"]
-git-tree-sha1 = "09ef0c32a26f80b465d808a1ba1e85775a282c97"
+git-tree-sha1 = "39f22411266cdd1621092c762a3f0648dbdc8433"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.17"
+version = "0.4.18"
 
 [[deps.JLLWrappers]]
 deps = ["Preferences"]
@@ -739,9 +739,9 @@ version = "1.3.0"
 
 [[deps.LayoutPointers]]
 deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"]
-git-tree-sha1 = "83b56449c39342a47f3fcdb3bc782bd6d66e1d97"
+git-tree-sha1 = "6dd77ee76188b0365f7d882d674b95796076fa2c"
 uuid = "10f19ff3-798f-405d-979b-55457f8fc047"
-version = "0.1.4"
+version = "0.1.5"
 
 [[deps.LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
@@ -1116,9 +1116,9 @@ version = "1.1.3"
 
 [[deps.PolyesterWeave]]
 deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"]
-git-tree-sha1 = "a3ff99bf561183ee20386aec98ab8f4a12dc724a"
+git-tree-sha1 = "0bc9e1a21ba066335a5207ac031ee41f72615181"
 uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad"
-version = "0.1.2"
+version = "0.1.3"
 
 [[deps.PolygonOps]]
 git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6"
@@ -1377,9 +1377,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[deps.SpecialFunctions]]
 deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "e08890d19787ec25029113e88c34ec20cac1c91e"
+git-tree-sha1 = "e6bf188613555c78062842777b116905a9f9dd49"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "2.0.0"
+version = "2.1.0"
 
 [[deps.StackViews]]
 deps = ["OffsetArrays"]

graphics/radial_distribution.jl

@@ -42,7 +42,7 @@ function gen_rdf_graphics()
 
             no_collision = true
 
-            if distance >= 2 * particle_radius
+            if distance >= 0.99 * 2 * particle_radius
                 for p2_ind in 1:(p1_ind - 1)
                     if ReCo.norm2d(p1_c - particle_cs[p2_ind]) < 2 * particle_radius
                         no_collision = false

graphics/verlet_and_cell_lists.jl

@@ -5,7 +5,7 @@ using StaticArrays: SVector
 using ReCo: ReCo
 
 function gen_verlet_and_cell_lists_graphics()
-    Random.seed!(2)
+    Random.seed!(23)
 
     box_length = 100
 
@@ -16,7 +16,7 @@ function gen_verlet_and_cell_lists_graphics()
     origin()
 
     R_particle = 4.2
-    σ = 2 * R_particle
+    σ = 2 * R_particle * 2^(-1 / 6)
     R_interaction = 2^(1 / 6) * σ
     R_skin = 2 * R_interaction
 
@@ -26,7 +26,7 @@ function gen_verlet_and_cell_lists_graphics()
     circle(Point(reference_particle_x, reference_particle_y), R_particle, :fill)
     reference_particle_c = SVector(reference_particle_x, reference_particle_y)
 
-    N = 92
+    N = 91
 
     particle_cs = Vector{SVector{2,Float64}}(undef, N)
 
@@ -43,7 +43,7 @@ function gen_verlet_and_cell_lists_graphics()
 
             no_collision = true
 
-            if distance >= 2 * R_particle
+            if distance >= 0.99 * 2 * R_particle
                 for p2_ind in 1:(p1_ind - 1)
                     if ReCo.norm2d(p1_c - particle_cs[p2_ind]) < 2 * R_particle
                         no_collision = false
@@ -59,7 +59,7 @@ function gen_verlet_and_cell_lists_graphics()
             end
         end
 
-        if 2 * R_particle <= distance < R_interaction
+        if distance < R_interaction
             setcolor("red")
         elseif R_interaction <= distance < R_skin
             setcolor("green")
@@ -91,4 +91,6 @@ function gen_verlet_and_cell_lists_graphics()
     finish()
 
     return nothing
-end
+end
+
+# TODO: Deduplicate with radial_distribution.jl

src/setup.jl

@@ -63,7 +63,7 @@ function gen_sim_consts(
     Dₜ = DEFAULT_Dₜ
     particle_radius = DEFAULT_PARTICLE_RADIUS
     Dᵣ = 3 * Dₜ / ((2 * particle_radius)^2)
-    σ = 2 * particle_radius
+    σ = 2 * particle_radius * 2^(-1 / 6)
     ϵ = DEFAULT_ϵ
     interaction_r = 2^(1 / 6) * σ