Refactoring

Examples/HydrogenAnion.jl

@@ -1,13 +1,14 @@
-using FewBodyPhysics
+using Revise
+using .FewBodyPhysics
 
-masses = [Inf, 1, 1]
+masses = [1e15, 1.0, 1.0]
 w_list = [ [1, -1, 0], [1, 0, -1], [0, 1, -1] ]
 
 K = [0 0 0; 0 1/2 0; 0 0 1/2]
-J, U = Ω(masses)
-K_transformedformed = J * K * J'
-w_transformedformedformed = [U' * w_list[i] for i in 1:length(w_list)]
+J, U = jacobi_transform(masses)
+K_transformed = J * K * J'
+w_transformed = [U' * w for w in w_list]
 Theortical_value = -0.527751016523
 
-p, Energy, bases = run_simulation(50, :quasirandom, w_transformedformedformed, K_transformedformed)
+p, Energy, bases = run_simulation(50, :quasirandom, w_transformed, K_transformed)
 

Examples/PionNucleon.jl

@@ -1,10 +1,11 @@
 using Plots
+using .FewBodyPhysics
 
 b = 3.9
 S = 41.5
 
 params = [b, S]
-masses = [(m_p+m_n)/2, m_π]
+masses = [(m_p+m_n)/2, m_pi]
 
 energies, Gaussians, eigenvectors, coordinates, masses = run_simulation_nuclear(5,2,5,masses,params)
 
@@ -16,7 +17,7 @@ grid_points = range(rmin,rmax,3000)
 
 Φ = zeros(length(grid_points), length(coordinates))
 
-for i in 1:length(coordinates)
+for i in eachindex(coordinates)
     local ϕ = zeros(length(grid_points))
     ϕ_sum = zeros(length(grid_points))
     rs = coordinates[i]

Examples/Positronium.jl

@@ -1,11 +1,12 @@
-using FewBodyPhysics
+using Revise
+using .FewBodyPhysics
 
 w_list = [ [1, -1, 0], [1, 0, -1], [0, 1, -1] ]
-masses = [1,1,1]
+masses = [1.0,1.0,1.0]
 K = [1/2 0 0; 0 1/2 0; 0 0 1/2]
-J, U = Ω(masses)
+J, U = jacobi_transform(masses)
 K_transformed = J * K * J'
-w_transformed = [U' * w_list[i] for i in 1:length(w_list)]
+w_transformed = [U' * w for w in w_list]
 
 Theortical_value = -0.2620050702328
 

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.4"
 manifest_format = "2.0"
-project_hash = "c019d638554320f1f902608dfe9771796da0203c"
+project_hash = "999ca58762a5dcddc22a862313696fe8b0c1610a"
 
 [[deps.ANSIColoredPrinters]]
 git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
@@ -16,9 +16,9 @@ version = "0.4.5"
 
 [[deps.Adapt]]
 deps = ["LinearAlgebra", "Requires"]
-git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099"
+git-tree-sha1 = "d80af0733c99ea80575f612813fa6aa71022d33a"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "4.0.4"
+version = "4.1.0"
 
     [deps.Adapt.extensions]
     AdaptStaticArraysExt = "StaticArrays"
@@ -83,6 +83,12 @@ git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642"
 uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
 version = "1.18.2+1"
 
+[[deps.CodeTracking]]
+deps = ["InteractiveUtils", "UUIDs"]
+git-tree-sha1 = "7eee164f122511d3e4e1ebadb7956939ea7e1c77"
+uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
+version = "1.3.6"
+
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
 git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759"
@@ -91,9 +97,9 @@ version = "0.7.6"
 
 [[deps.ColorSchemes]]
 deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"]
-git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0"
+git-tree-sha1 = "13951eb68769ad1cd460cdb2e64e5e95f1bf123d"
 uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-version = "3.26.0"
+version = "3.27.0"
 
 [[deps.ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
@@ -409,9 +415,9 @@ version = "0.10.2+0"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
-git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed"
+git-tree-sha1 = "bc3f416a965ae61968c20d0ad867556367f2817d"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "1.10.8"
+version = "1.10.9"
 
 [[deps.HarfBuzz_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"]
@@ -458,6 +464,12 @@ git-tree-sha1 = "25ee0be4d43d0269027024d75a24c24d6c6e590c"
 uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
 version = "3.0.4+0"
 
+[[deps.JuliaInterpreter]]
+deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"]
+git-tree-sha1 = "2984284a8abcfcc4784d95a9e2ea4e352dd8ede7"
+uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a"
+version = "0.9.36"
+
 [[deps.LAME_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd"
@@ -543,9 +555,9 @@ version = "3.2.2+1"
 
 [[deps.Libgcrypt_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"]
-git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673"
+git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b"
 uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4"
-version = "1.8.11+0"
+version = "1.11.0+0"
 
 [[deps.Libglvnd_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"]
@@ -555,15 +567,15 @@ version = "1.6.0+0"
 
 [[deps.Libgpg_error_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed"
+git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6"
 uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8"
-version = "1.49.0+0"
+version = "1.50.0+0"
 
 [[deps.Libiconv_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175"
+git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269"
 uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
-version = "1.17.0+0"
+version = "1.17.0+1"
 
 [[deps.Libmount_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -614,9 +626,15 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[deps.LoggingExtras]]
 deps = ["Dates", "Logging"]
-git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075"
+git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3"
 uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36"
-version = "1.0.3"
+version = "1.1.0"
+
+[[deps.LoweredCodeUtils]]
+deps = ["JuliaInterpreter"]
+git-tree-sha1 = "260dc274c1bc2cb839e758588c63d9c8b5e639d1"
+uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b"
+version = "3.0.5"
 
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
@@ -783,9 +801,9 @@ version = "1.10.0"
 
 [[deps.PlotThemes]]
 deps = ["PlotUtils", "Statistics"]
-git-tree-sha1 = "6e55c6841ce3411ccb3457ee52fc48cb698d6fb0"
+git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca"
 uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
-version = "3.2.0"
+version = "3.3.0"
 
 [[deps.PlotUtils]]
 deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"]
@@ -902,6 +920,12 @@ git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7"
 uuid = "ae029012-a4dd-5104-9daa-d747884805df"
 version = "1.3.0"
 
+[[deps.Revise]]
+deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "REPL", "Requires", "UUIDs", "Unicode"]
+git-tree-sha1 = "7f4228017b83c66bd6aa4fddeb170ce487e53bc7"
+uuid = "295af30f-e4ad-537b-8983-00126c2a3abe"
+version = "3.6.2"
+
 [[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 version = "0.7.0"
@@ -1090,9 +1114,9 @@ version = "1.31.0+0"
 
 [[deps.XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
-git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127"
+git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
-version = "2.13.3+0"
+version = "2.13.4+0"
 
 [[deps.XSLT_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"]
@@ -1102,9 +1126,9 @@ version = "1.1.41+0"
 
 [[deps.XZ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632"
+git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc"
 uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
-version = "5.4.6+0"
+version = "5.6.3+0"
 
 [[deps.Xorg_libICE_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]

Project.toml

@@ -9,6 +9,7 @@ DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 
 [compat]
 Documenter = "1.1.2"

docs/src/API.md

@@ -2,13 +2,14 @@
 
 ## Coordinates
 ```@docs
-Ω
-A_generate
+ParticleSystem
+jacobi_transform
+generate_A_matrix
 transform_list
-shift
-w_gen
+shift_vectors
+generate_weight_vector
 transform_coordinates
-transform_back
+inverse_transform_coordinates
 ```
 
 ## Matrix elements
@@ -29,6 +30,12 @@ OptimizeGlobalParameters
 ```@docs
 corput
 halton
+calculate_energies
 run_simulation
 run_simulation_nuclear
 ```
+## Constants
+
+```@docs
+μ
+```

docs/src/examples.md

@@ -5,16 +5,16 @@ Suppose you want to calculate the ground state energy of the hydrogen anion in t
 ```@example example1
 using Plots, FewBodyPhysics
 
-masses = [Inf, 1, 1]
+masses = [1e15, 1.0, 1.0]
 w_list = [ [1, -1, 0], [1, 0, -1], [0, 1, -1] ]
 
 K = [0 0 0; 0 1/2 0; 0 0 1/2]
-J, U = Ω(masses)
-K_transformedformed = J * K * J'
-w_transformedformedformed = [U' * w_list[i] for i in 1:length(w_list)]
+J, U = jacobi_transform(masses)
+K_transformed = J * K * J'
+w_transformed = [U' * w for w in w_list]
 Theortical_value = -0.527751016523
 
-p, Energy, bases = run_simulation(50, :quasirandom, w_transformedformedformed, K_transformedformed)
+p, Energy, bases = run_simulation(50, :quasirandom, w_transformed, K_transformed)
 plot(p)
 ```
 

docs/src/index.md

@@ -16,40 +16,42 @@ H = - \sum_{i=1}^{3} \frac{1}{2m_i}\frac{\partial^2}{\partial \boldsymbol{r}_i^2
 ```
 The masses of the three constituents are `m_i = {1, 1, 1}` and the charges `q_i = {+1, −1, −1}`. We can estimate the ground state of this Coulombic three-body system using 50 Gaussians
 
-### Psudorandom
+### Quasirandom
 
 ```@example 1
 using Plots, FewBodyPhysics
 
 w_list = [ [1, -1, 0], [1, 0, -1], [0, 1, -1] ]
-masses = [1,1,1]
+masses = [1.0,1.0,1.0]
 K = [1/2 0 0; 0 1/2 0; 0 0 1/2]
-J, U = Ω(masses)
+J, U = jacobi_transform(masses)
 K_transformed = J * K * J'
-w_transformed = [U' * w_list[i] for i in 1:length(w_list)]
+w_transformed = [U' * w for w in w_list]
+
 Theortical_value = -0.2620050702328
 
-p, Energy = run_simulation(50,:psudorandom, w_transformed, K_transformed)
+p, Energy = run_simulation(50,:quasirandom, w_transformed, K_transformed)
 plot(p)
 ```
 With a difference in energy
 ```@example 1
-@show Theortical_value - Energy
+@show Energy-Theortical_value
 ```
-### Quasirandom
+### Psudorandom
 And similarly for a quasirandom
 ```@example 2
 using Plots, FewBodyPhysics
 
 w_list = [ [1, -1, 0], [1, 0, -1], [0, 1, -1] ]
-masses = [1,1,1]
+masses = [1.0,1.0,1.0]
 K = [1/2 0 0; 0 1/2 0; 0 0 1/2]
-J, U = Ω(masses)
+J, U = jacobi_transform(masses)
 K_transformed = J * K * J'
-w_transformed = [U' * w_list[i] for i in 1:length(w_list)]
+w_transformed = [U' * w for w in w_list]
+
 Theortical_value = -0.2620050702328
 
-p, Energy = run_simulation(50,:quasirandom, w_transformed, K_transformed)
+p, Energy = run_simulation(50,:psudorandom, w_transformed, K_transformed)
 plot(p)
 ```
 With a difference in energy
@@ -68,7 +70,7 @@ b = 3.9
 S = 41.5
 
 params = [b, S]
-masses = [(m_p+m_n)/2, m_π]
+masses = [(m_p+m_n)/2, m_pi]
 
 energies, Gaussians, eigenvectors, coordinates, masses = run_simulation_nuclear(5,2,5,masses,params)
 
@@ -80,7 +82,7 @@ grid_points = range(rmin,rmax,3000)
 
 Φ = zeros(length(grid_points), length(coordinates))
 
-for i in 1:length(coordinates)
+for i in eachindex(coordinates)
     local ϕ = zeros(length(grid_points))
     ϕ_sum = zeros(length(grid_points))
     rs = coordinates[i]

src/FewBodyPhysics.jl

@@ -1,15 +1,13 @@
 module FewBodyPhysics
 
-using LinearAlgebra, Plots
+export m_pi, m_pi0, m_p, m_n, μ, ħc, m_bare
+export jacobi_transform, generate_A_matrix, transform_list, shift_vectors, generate_weight_vector, transform_coordinates, inverse_transform_coordinates
+export S_elements, S_wave, S_energy, P_elements, pion_nucleon, ComputeEigenSystem, GetMinimumEnergy, OptimizeGlobalParameters
+export corput, halton, calculate_energies, run_simulation, run_simulation_nuclear
 
+include("constants.jl")
 include("coordinates.jl")
 include("matrix_elements.jl")
 include("sampling.jl")
-include("constants.jl")
-
-export m_π, m_π0, m_p, m_n, μ, m, ħc, mbare
-export Ω, A_generate, transform_list, shift, w_gen, transform_coordinates, transform_back
-export S_elements, S_wave, S_energy, P_elements, pion_nucleon, ComputeEigenSystem, GetMinimumEnergy, OptimizeGlobalParameters
-export corput, halton, run_simulation, run_simulation_nuclear
 
 end