From 1003ccf851a583cf1ac08b5d899af8b268bcab7c Mon Sep 17 00:00:00 2001
From: Mo8it <mo8it@protonmail.com>
Date: Tue, 25 Jan 2022 22:15:42 +0100
Subject: [PATCH] Fixed rdf

---
 Manifest.toml                                 |  14 +-
 ...g_of_r_d_ratio_with_0_37_packing_ratio.csv | 221 ++++++++++++++++++
 ...g_of_r_d_ratio_with_0_45_packing_ratio.csv | 149 ------------
 .../radial_distribution_function.jl           |  34 +--
 src/setup.jl                                  |   4 +-
 5 files changed, 247 insertions(+), 175 deletions(-)
 create mode 100644 analysis/radial_distribution_function/g_of_r_d_ratio_with_0_37_packing_ratio.csv
 delete mode 100644 analysis/radial_distribution_function/g_of_r_d_ratio_with_0_45_packing_ratio.csv

diff --git a/Manifest.toml b/Manifest.toml
index 93c2adc..2ecb052 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -467,10 +467,10 @@ uuid = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 version = "0.5.1"
 
 [[deps.GPUArrays]]
-deps = ["Adapt", "LinearAlgebra", "Printf", "Random", "Serialization", "Statistics"]
-git-tree-sha1 = "d9681e61fbce7dde48684b40bdb1a319c4083be7"
+deps = ["Adapt", "LLVM", "LinearAlgebra", "Printf", "Random", "Serialization", "Statistics"]
+git-tree-sha1 = "cf91e6e9213b9190dc0511d6fff862a86652a94a"
 uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "8.1.3"
+version = "8.2.1"
 
 [[deps.GPUCompiler]]
 deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"]
@@ -945,9 +945,9 @@ version = "0.7.3"
 
 [[deps.ModernGL]]
 deps = ["Libdl"]
-git-tree-sha1 = "1b4ca9b2956401690dfbf1b49e345ca539b54b03"
+git-tree-sha1 = "344f8896e55541e30d5ccffcbf747c98ad57ca47"
 uuid = "66fc600b-dfda-50eb-8b99-91cfa97b1301"
-version = "1.1.3"
+version = "1.1.4"
 
 [[deps.MosaicViews]]
 deps = ["MappedArrays", "OffsetArrays", "PaddedViews", "StackViews"]
@@ -1153,9 +1153,9 @@ uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
 
 [[deps.ProfileView]]
 deps = ["Cairo", "Colors", "FileIO", "FlameGraphs", "Graphics", "Gtk", "GtkObservables", "InteractiveUtils", "IntervalSets", "MethodAnalysis", "Preferences", "Profile", "UUIDs"]
-git-tree-sha1 = "6a9fe54afc52e4b98029e15dbd0552d82a2c5b94"
+git-tree-sha1 = "93b795da19d3668ff3ba5463481d137ba7fb3c2a"
 uuid = "c46f51b8-102a-5cf2-8d2c-8597cb0e0da7"
-version = "1.3.1"
+version = "1.4.0"
 
 [[deps.ProgressMeter]]
 deps = ["Distributed", "Printf"]
diff --git a/analysis/radial_distribution_function/g_of_r_d_ratio_with_0_37_packing_ratio.csv b/analysis/radial_distribution_function/g_of_r_d_ratio_with_0_37_packing_ratio.csv
new file mode 100644
index 0000000..307c866
--- /dev/null
+++ b/analysis/radial_distribution_function/g_of_r_d_ratio_with_0_37_packing_ratio.csv
@@ -0,0 +1,221 @@
+# Source: https://arxiv.org/abs/1305.4185
+# Figure 2a (repulsive part)
+r_d_ratio,g_of_r_d_ratio
+0.0,0.0
+0.96164,0.02786
+0.9636,0.05169
+0.96512,0.07895
+0.96598,0.09856
+0.96706,0.12817
+0.96784,0.15225
+0.9686,0.17769
+0.96907,0.19467
+0.96977,0.2209
+0.97045,0.24789
+0.97088,0.26584
+0.9715,0.29227
+0.97209,0.31884
+0.97266,0.34494
+0.973,0.36144
+0.97349,0.38545
+0.97409,0.41577
+0.97448,0.43706
+0.97485,0.4579
+0.97531,0.48519
+0.97563,0.50565
+0.97605,0.53368
+0.97637,0.55542
+0.9767,0.5783
+0.97705,0.60237
+0.97742,0.62761
+0.9778,0.65412
+0.97806,0.67228
+0.97846,0.69978
+0.97874,0.71947
+0.97915,0.74789
+0.97943,0.76801
+0.97987,0.7982
+0.98015,0.81826
+0.98046,0.83951
+0.98091,0.8711
+0.9812,0.89179
+0.98151,0.91314
+0.98182,0.93526
+0.9823,0.96875
+0.9826,0.99014
+0.9829,1.01183
+0.98321,1.03383
+0.98352,1.05614
+0.98384,1.07882
+0.98415,1.10194
+0.9846,1.13513
+0.98489,1.15685
+0.98518,1.17867
+0.98547,1.20062
+0.98575,1.22282
+0.98604,1.24547
+0.98643,1.27759
+0.98668,1.29838
+0.98693,1.31941
+0.98717,1.3411
+0.98749,1.37117
+0.98769,1.39103
+0.98799,1.4212
+0.98816,1.43999
+0.98842,1.46943
+0.98858,1.4877
+0.98881,1.51643
+0.98896,1.53465
+0.98918,1.56293
+0.98933,1.58148
+0.98955,1.60964
+0.98971,1.62871
+0.98994,1.65717
+0.99011,1.67668
+0.99038,1.70607
+0.99061,1.72559
+0.99108,1.75567
+0.9915,1.77461
+0.99241,1.80404
+0.99318,1.82202
+0.9948,1.84898
+0.99706,1.87388
+1.00018,1.89554
+1.00644,1.91739
+1.02588,1.91493
+1.03854,1.89243
+1.05122,1.86333
+1.06076,1.83878
+1.06695,1.82204
+1.07627,1.79596
+1.08567,1.76895
+1.09166,1.75157
+1.10064,1.72551
+1.10949,1.70024
+1.11802,1.67669
+1.12623,1.65491
+1.13425,1.63457
+1.14478,1.60937
+1.15521,1.58598
+1.16575,1.56367
+1.17662,1.54153
+1.18805,1.51868
+1.20011,1.49464
+1.20946,1.47603
+1.22195,1.45125
+1.23452,1.42643
+1.24686,1.40221
+1.25576,1.38489
+1.26961,1.35834
+1.28181,1.33561
+1.29262,1.31644
+1.30701,1.29284
+1.32042,1.27245
+1.33623,1.24913
+1.35114,1.22743
+1.36684,1.20483
+1.38272,1.18229
+1.39815,1.16079
+1.41519,1.13777
+1.43063,1.11803
+1.44812,1.09736
+1.46689,1.07698
+1.48837,1.05493
+1.50839,1.0351
+1.52903,1.01524
+1.54947,0.99615
+1.57224,0.97577
+1.59447,0.95741
+1.62068,0.93843
+1.64551,0.92314
+1.67523,0.90722
+1.70718,0.89197
+1.73659,0.87931
+1.77156,0.86746
+1.80855,0.86016
+1.84519,0.85849
+1.88439,0.86139
+1.92032,0.8688
+1.9503,0.88389
+1.97435,0.90228
+1.99621,0.92162
+2.0194,0.94113
+2.04386,0.95977
+2.06806,0.97691
+2.09549,0.99406
+2.12575,1.00839
+2.15951,1.02065
+2.19533,1.03215
+2.22914,1.04031
+2.26856,1.04517
+2.30741,1.04651
+2.34319,1.04605
+2.38102,1.04457
+2.42199,1.04218
+2.45815,1.03938
+2.49681,1.03527
+2.53604,1.03007
+2.57029,1.02504
+2.61109,1.01866
+2.64646,1.01281
+2.68495,1.00623
+2.72073,1.00032
+2.75703,0.99521
+2.79567,0.99138
+2.83291,0.98871
+2.87019,0.98648
+2.91148,0.98494
+2.95074,0.98421
+2.98565,0.98414
+3.02438,0.985
+3.06253,0.98701
+3.10261,0.98965
+3.13977,0.99201
+3.17689,0.99414
+3.21799,0.99623
+3.25632,0.99799
+3.29591,0.99968
+3.33017,1.00105
+3.36996,1.00251
+3.40917,1.00378
+3.44734,1.0048
+3.48395,1.00552
+3.52307,1.00603
+3.56237,1.0063
+3.60025,1.00627
+3.63863,1.00577
+3.67946,1.00484
+3.71481,1.00392
+3.75646,1.00287
+3.79209,1.00211
+3.8327,1.0014
+3.8704,1.0008
+3.90587,1.00023
+3.94426,0.99959
+3.98355,0.99897
+4.02159,0.99846
+4.06123,0.99813
+4.10093,0.99822
+4.14072,0.99854
+4.17676,0.99881
+4.22138,0.99907
+4.25186,0.9992
+4.29599,0.99935
+4.33118,0.99946
+4.36795,0.99957
+4.40578,0.99968
+4.44436,0.99979
+4.48347,0.9999
+4.52299,1.00002
+4.56276,1.00014
+4.60262,1.00028
+4.64249,1.00042
+4.68236,1.00058
+4.72224,1.00074
+4.76211,1.00091
+4.78846,1.00102
+4.82784,1.0012
+4.86729,1.00138
+4.90678,1.00156
+4.94633,1.00175
+4.98591,1.00193
diff --git a/analysis/radial_distribution_function/g_of_r_d_ratio_with_0_45_packing_ratio.csv b/analysis/radial_distribution_function/g_of_r_d_ratio_with_0_45_packing_ratio.csv
deleted file mode 100644
index 39928d0..0000000
--- a/analysis/radial_distribution_function/g_of_r_d_ratio_with_0_45_packing_ratio.csv
+++ /dev/null
@@ -1,149 +0,0 @@
-# Source: https://www.researchgate.net/publication/223333736_Reconstruction_of_Ross'_linear-mixing_model_for_the_equation_of_state_of_deuterium
-r_d_ratio,g_of_r_d_ratio
-0.99392,0.08604
-0.99388,0.18421
-0.99384,0.28847
-0.99382,0.34463
-0.99378,0.42994
-0.99372,0.52947
-0.99365,0.63441
-0.99361,0.68891
-0.99354,0.77406
-0.99344,0.87468
-0.99332,0.98013
-0.99325,1.03317
-0.99314,1.11822
-0.99297,1.21964
-0.99278,1.32539
-0.99267,1.37722
-0.99249,1.4622
-0.99224,1.56412
-0.99194,1.67
-0.99179,1.72089
-0.99152,1.8058
-0.99116,1.90793
-0.99074,2.01372
-0.99053,2.06399
-0.99015,2.1488
-0.98965,2.25086
-0.98909,2.35636
-0.98881,2.40637
-0.98831,2.49108
-0.98767,2.5925
-0.98699,2.69664
-0.98665,2.74669
-0.98607,2.83091
-0.98538,2.92885
-0.98467,3.02834
-0.98395,3.12761
-0.98362,3.17414
-0.98304,3.25677
-0.98242,3.34772
-0.98183,3.43776
-0.98129,3.52581
-0.98081,3.61118
-0.98043,3.69358
-0.98015,3.77322
-0.98,3.85156
-0.98014,3.95169
-0.98089,4.03823
-0.98357,4.10894
-0.9944,4.032
-1.00014,3.93792
-1.00441,3.85868
-1.00862,3.77571
-1.01272,3.69218
-1.01669,3.61072
-1.0216,3.51176
-1.02638,3.42062
-1.03128,3.33517
-1.03664,3.25085
-1.04281,3.16285
-1.04804,3.09295
-1.05614,2.98982
-1.06293,2.90588
-1.07039,2.81547
-1.07549,2.75441
-1.08352,2.65945
-1.09202,2.56047
-1.09758,2.49642
-1.10625,2.39796
-1.11214,2.33189
-1.12071,2.23742
-1.12939,2.14379
-1.13793,2.05435
-1.14612,1.97171
-1.15388,1.89756
-1.16359,1.81176
-1.17456,1.72585
-1.18615,1.64833
-1.19996,1.56268
-1.21169,1.47967
-1.22345,1.39143
-1.23543,1.30583
-1.24773,1.23043
-1.26375,1.14911
-1.28235,1.06205
-1.30026,0.97628
-1.32001,0.89731
-1.34607,0.8185
-1.38029,0.74139
-1.42373,0.67706
-1.47928,0.62965
-1.54985,0.64005
-1.60887,0.68208
-1.65956,0.742
-1.70693,0.80174
-1.75549,0.86677
-1.7997,0.93281
-1.8408,0.99879
-1.88278,1.07151
-1.92418,1.14479
-1.96069,1.20961
-2.00089,1.27998
-2.06624,1.29427
-2.12188,1.24296
-2.16454,1.1732
-2.20365,1.10578
-2.2468,1.03273
-2.28968,0.97094
-2.34711,0.92061
-2.40659,0.87706
-2.47617,0.86598
-2.54506,0.87775
-2.6091,0.91495
-2.67198,0.9548
-2.73415,0.99707
-2.79524,1.03776
-2.86004,1.06782
-2.92949,1.08716
-2.99726,1.09694
-3.06572,1.07401
-3.13305,1.0512
-3.20406,1.01975
-3.26722,0.99225
-3.33163,0.96833
-3.40415,0.95312
-3.46976,0.95561
-3.53944,0.96948
-3.61034,0.98695
-3.68191,1.00826
-3.74431,1.02656
-3.81351,1.04126
-3.88832,1.04634
-3.95948,1.04227
-4.02721,1.03357
-4.09307,1.02294
-4.16757,1.01022
-4.23256,0.99784
-4.30367,0.98757
-4.3786,0.98803
-4.44527,0.99118
-4.51289,0.99726
-4.58223,1.00774
-4.65288,1.01261
-4.72314,1.01386
-4.79174,1.02311
-4.86131,1.03134
-4.93191,1.0253
-4.98585,1.01943
diff --git a/analysis/radial_distribution_function/radial_distribution_function.jl b/analysis/radial_distribution_function/radial_distribution_function.jl
index dea9ae9..7eed4f2 100644
--- a/analysis/radial_distribution_function/radial_distribution_function.jl
+++ b/analysis/radial_distribution_function/radial_distribution_function.jl
@@ -163,7 +163,7 @@ function plot_radial_distributions(
         yticks=0:ceil(Int64, max_g),
         xlabel=L"r / d",
         ylabel=L"g",
-        limits=(min_lower_radius, max_lower_radius, min_g, max_g),
+        limits=(min_lower_radius - 0.03, max_lower_radius + 0.03, min_g, max_g * 1.03),
     )
 
     lines!(
@@ -175,25 +175,25 @@ function plot_radial_distributions(
         linewidth=1,
     )
 
-    expected = CSV.read(
-        "analysis/radial_distribution_function/g_of_r_d_ratio_with_0_45_packing_ratio.csv",
-        DataFrames.DataFrame;
-        header=2,
-    )
-    lines!(
-        ax,
-        expected.r_d_ratio,
-        expected.g_of_r_d_ratio;
-        label="Expectation for dense hard spheres",
-        color=:green,
-    )
-
     for (g_ind, g) in enumerate(gs)
         scatterlines!(
             ax, lower_radii, g; markersize=3, linewidth=0.5, label=L"v_0 = %$(v₀s[g_ind])"
         )
     end
 
+    comparison_curve = CSV.read(
+        "analysis/radial_distribution_function/g_of_r_d_ratio_with_0_37_packing_ratio.csv",
+        DataFrames.DataFrame;
+        header=3,
+    )
+    lines!(
+        ax,
+        comparison_curve.r_d_ratio,
+        comparison_curve.g_of_r_d_ratio;
+        label="Similar system",
+        color=:green,
+    )
+
     axislegend(ax; position=:rt, padding=3, rowgap=-3)
 
     save_fig("radial_distribution.pdf", fig)
@@ -202,16 +202,16 @@ function plot_radial_distributions(
 end
 
 function run_radial_distribution_analysis()
-    v₀s = (0.0, 80.0)
+    v₀s = (0.0, 20.0)
 
     n_particles = 1000
 
     sim_dirs = radial_distribution_simulation(;
-        n_particles=n_particles, v₀s=v₀s, T=100.0, packing_ratio=0.45
+        n_particles=n_particles, v₀s=v₀s, T=100.0, packing_ratio=0.37
     )
 
     lower_radii, gs, particle_radius = radial_distribution(;
-        sim_dirs=sim_dirs, n_radii=75, n_last_snapshots=200, n_particles=n_particles
+        sim_dirs=sim_dirs, n_radii=56, n_last_snapshots=200, n_particles=n_particles
     )
 
     plot_radial_distributions(v₀s, lower_radii, gs, particle_radius)
diff --git a/src/setup.jl b/src/setup.jl
index 42048cf..c2b040b 100644
--- a/src/setup.jl
+++ b/src/setup.jl
@@ -1,6 +1,6 @@
 const DEFAULT_PACKING_RATIO = 0.5
 const DEFAULT_δt = 1e-5
-const DEFAULT_SKIN_TO_INTERACTION_R_RATIO = 1.5
+const DEFAULT_SKIN_TO_INTERACTION_R_RATIO = 2.0
 const DEFAULT_EXPORTS_DIR = "exports"
 const DEFAULT_PARENT_DIR = ""
 const DEFAULT_COMMENT = ""
@@ -67,7 +67,7 @@ function gen_sim_consts(
     ϵ = DEFAULT_ϵ
     interaction_r = 2^(1 / 6) * σ
 
-    buffer = 1.8
+    buffer = 2.5
     max_approach_after_one_integration_step = buffer * (2 * v₀ * δt) / interaction_r
     @assert skin_to_interaction_r_ratio >= 1 + max_approach_after_one_integration_step