Reorganize dependency structure

NuclearRMF.jl

@@ -0,0 +1,56 @@
+using PolyLog, Plots
+include("nucleons.jl")
+include("mesons.jl")
+
+"Total binding energy of the system"
+total_E(s::system, Es_p, occs_p, Es_n, occs_n) = sum(occs_p .* (M_p .- Es_p)) + sum(occs_n .* (M_n .- Es_n)) - meson_E(s)
+
+"Normalized Woods-Saxon form used for constructing an initial solution"
+Woods_Saxon(r::Float64; R::Float64=7.0, a::Float64=0.5) = -1 / (8π * a^3 * reli3(-exp(R / a)) * (1 + exp((r - R) / a)))
+
+"Run the full program by self-consistent solution of nucleon and meson densities"
+function solve_system(s::system; reinitialize_densities=true, monitor_print=true, monitor_plot=false)
+    if reinitialize_densities
+        dens_guess = Woods_Saxon.(rs(s))
+        @. s.ρ_sp = s.Z * dens_guess
+        @. s.ρ_vp = s.Z * dens_guess
+        @. s.ρ_sn = s.N * dens_guess
+        @. s.ρ_vn = s.N * dens_guess
+    end
+
+    if monitor_plot
+        p = plot(legends=false, size=(1024, 768), layout=(2, 4), title=["ρₛₚ" "ρᵥₚ" "ρₛₙ" "ρᵥₙ" "Φ₀" "W₀" "B₀" "A₀"])
+    end
+
+    previous_E_per_A = NaN
+
+    while true
+        # mesons
+        @time "Meson fields" solveMesonFields!(s, isnan(previous_E_per_A) ? 50 : 15)
+
+        # protons
+        @time "Proton spectrum" (κs_p, Es_p) = findAllOrbitals(true, s)
+        occs_p = fillNucleons(s.Z, κs_p, Es_p)
+        @time "Proton densities" (s.ρ_sp, s.ρ_vp) = calculateNucleonDensity(κs_p, Es_p, occs_p, true, s)
+
+        # neutrons
+        @time "Neutron spectrum" (κs_n, Es_n) = findAllOrbitals(false, s)
+        occs_n = fillNucleons(s.N, κs_n, Es_n)
+        @time "Neutron densities" (s.ρ_sn, s.ρ_vn) = calculateNucleonDensity(κs_n, Es_n, occs_n, false, s)
+
+        if monitor_plot
+            for s in p.series_list
+                s.plotattributes[:linecolor] = :gray
+            end
+            plot!(p, rs(s), hcat(s.ρ_sp, s.ρ_vp, s.ρ_sn, s.ρ_vn, s.Φ0, s.W0, s.B0, s.A0), linecolor=:red)
+            display(p)
+        end
+
+        E_per_A = total_E(s, Es_p, occs_p, Es_n, occs_n) / A(s)
+        monitor_print && println("Total binding E per nucleon = $E_per_A")
+
+        # check convergence
+        abs(previous_E_per_A - E_per_A) < 0.0001 && break
+        previous_E_per_A = E_per_A
+    end
+end

common.jl

@@ -0,0 +1,2 @@
+const ħc = 197.33 # MeVfm
+const r_reg = 1E-8 # fm # regulator for R

mesons.jl

@@ -1,6 +1,5 @@
-using DifferentialEquations
-
-const ħc = 197.33 # MeVfm
+include("common.jl")
+include("system.jl")
 
 # Values defined in C. J. Horowitz and J. Piekarewicz, Phys. Rev. Lett. 86, 5647 (2001)
 # Values taken from Hartree.f (FSUGarnet)
@@ -17,8 +16,6 @@ const λ = -0.003551486718 # dimensionless # LambdaSS
 const ζ = 0.023499504053 # dimensionless # LambdaVV
 const Λv = 0.043376933644 # dimensionless # LambdaVR
 
-const r_reg = 1E-8 # fm # regulator for Green's functions
-
 "Green's function for Klein-Gordon equation in natural units"
 greensFunctionKG(m, r, rp) = -1 / (m * (r + r_reg) * (rp + r_reg)) * sinh(m * min(r, rp)) * exp(-m * max(r, rp))
 

nucleons.jl

@@ -1,12 +1,11 @@
 using DifferentialEquations
 include("bisection.jl")
+include("common.jl")
+include("system.jl")
 
-const ħc = 197.33 # MeVfm
 const M_n = 939.0 # MeV/c2
 const M_p = 939.0 # MeV/c2
 
-const r_reg = 1E-8 # fm # regulator for the centrifugal term
-
 "The spherical Dirac equation that returns du=[dg, df] in-place where
     u=[g, f] are the reduced radial components evaluated at r,
     κ is the generalized angular momentum,

system.jl

@@ -1,4 +1,4 @@
-using Interpolations, PolyLog, Plots
+using Interpolations
 
 "Defines a nuclear system containing relevant parameters and meson/nucleon densities"
 mutable struct system
@@ -40,9 +40,6 @@ Z_or_N(s::system, p::Bool)::Int = p ? s.Z : s.N
 "Create an empty array for the size of the mesh"
 zero_array(s::system) = zeros(1 + s.divs)
 
-"Normalized Woods-Saxon form used for constructing an initial solution"
-Woods_Saxon(r::Float64; R::Float64=7.0, a::Float64=0.5) = -1 / (8π * a^3 * reli3(-exp(R / a)) * (1 + exp((r - R) / a)))
-
 "Create linear interpolations for the meson fields"
 function fields_interp(s::system)
     S_interp = linear_interpolation(rs(s), s.Φ0)
@@ -51,56 +48,3 @@ function fields_interp(s::system)
     A_interp = linear_interpolation(rs(s), s.A0)
     return (S_interp, V_interp, R_interp, A_interp)
 end
-
-include("nucleons.jl")
-include("mesons.jl")
-
-"Run the full program by self-consistent solution of nucleon and meson densities"
-function solve_system(s::system; reinitialize_densities=true, monitor_print=true, monitor_plot=false)
-    if reinitialize_densities
-        dens_guess = Woods_Saxon.(rs(s))
-        @. s.ρ_sp = s.Z * dens_guess
-        @. s.ρ_vp = s.Z * dens_guess
-        @. s.ρ_sn = s.N * dens_guess
-        @. s.ρ_vn = s.N * dens_guess
-    end
-
-    if monitor_plot
-        p = plot(legends=false, size=(1024, 768), layout=(2, 4), title=["ρₛₚ" "ρᵥₚ" "ρₛₙ" "ρᵥₙ" "Φ₀" "W₀" "B₀" "A₀"])
-    end
-
-    previous_E_per_A = NaN
-
-    while true
-        # mesons
-        @time "Meson fields" solveMesonFields!(s, isnan(previous_E_per_A) ? 50 : 15)
-
-        # protons
-        @time "Proton spectrum" (κs_p, Es_p) = findAllOrbitals(true, s)
-        occs_p = fillNucleons(s.Z, κs_p, Es_p)
-        @time "Proton densities" (s.ρ_sp, s.ρ_vp) = calculateNucleonDensity(κs_p, Es_p, occs_p, true, s)
-
-        # neutrons
-        @time "Neutron spectrum" (κs_n, Es_n) = findAllOrbitals(false, s)
-        occs_n = fillNucleons(s.N, κs_n, Es_n)
-        @time "Neutron densities" (s.ρ_sn, s.ρ_vn) = calculateNucleonDensity(κs_n, Es_n, occs_n, false, s)
-
-        if monitor_plot
-            for s in p.series_list
-                s.plotattributes[:linecolor] = :gray
-            end
-            plot!(p, rs(s), hcat(s.ρ_sp, s.ρ_vp, s.ρ_sn, s.ρ_vn, s.Φ0, s.W0, s.B0, s.A0), linecolor=:red)
-            display(p)
-        end
-
-        E_per_A = total_E(s, Es_p, occs_p, Es_n, occs_n) / A(s)
-        monitor_print && println("Total binding E per nucleon = $E_per_A")
-
-        # check convergence
-        abs(previous_E_per_A - E_per_A) < 0.0001 && break
-        previous_E_per_A = E_per_A
-    end
-end
-
-"Total binding energy of the system"
-total_E(s::system, Es_p, occs_p, Es_n, occs_n) = sum(occs_p .* (M_p .- Es_p)) + sum(occs_n .* (M_n .- Es_n)) - meson_E(s)

test/Linear_nucleon_spectrum.jl

@@ -1,5 +1,5 @@
-using DelimitedFiles, Interpolations, Plots
-include("../system.jl")
+using DelimitedFiles, Plots
+include("../nucleons.jl")
 
 # test data generated from Hartree.f
 # format: x S(x) V(x) R(x) A(x)

test/Pb208.jl

@@ -1,4 +1,4 @@
-include("../system.jl")
+include("../NuclearRMF.jl")
 
 s = system(82, 126, 20.0, 400)
 

test/Pb208_meson_flds.jl

@@ -1,5 +1,5 @@
-using DelimitedFiles, Interpolations, Plots
-include("../system.jl")
+using DelimitedFiles, Plots
+include("../mesons.jl")
 
 # test data generated from Hartree.f
 # format: x S(x) V(x) R(x) A(x)

test/Pb208_nucleon_dens.jl

@@ -1,5 +1,5 @@
 using DelimitedFiles, Plots
-include("../system.jl")
+include("../nucleons.jl")
 
 # test data generated from Hartree.f
 # format: x S(x) V(x) R(x) A(x)

test/Pb208_nucleon_spectrum.jl

@@ -1,5 +1,5 @@
-using DelimitedFiles, Interpolations, Plots
-include("../system.jl")
+using DelimitedFiles, Plots
+include("../nucleons.jl")
 
 # test data generated from Hartree.f
 # format: x S(x) V(x) R(x) A(x)

test/Pb208_nucleon_wf.jl

@@ -1,5 +1,5 @@
-using DelimitedFiles, Interpolations, Plots
-include("../system.jl")
+using DelimitedFiles, Plots
+include("../nucleons.jl")
 
 # test data generated from Hartree.f
 # format: x S(x) V(x) R(x) A(x)

test/Pb208_shooting.jl

@@ -1,5 +1,5 @@
 using DelimitedFiles, Plots
-include("../system.jl")
+include("../nucleons.jl")
 
 # test data generated from Hartree.f
 # format: x S(x) V(x) R(x) A(x)