Cleaned up and added comparisons against established implementations

.gitignore

@@ -76,4 +76,6 @@ Manifest.toml
 # Original notes from when developing
 notes/*
 # My terrible, newbie attempt at version control (yes, shouldve jsut learned git)
-backups/*
+backups/*
+# Directory for holding the code for various bhmie implementations
+.bhmielibs/*

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "GitHooks.hooksDirectory": "/home/cianh/Programming/Git_Projects/nanoconc/.git/hooks"
+}

0-100abs.jl

@@ -1,24 +0,0 @@
-include("nanoconc.jl")
-using PyPlot
-
-particledata = ([2.5 1.],
-                [5. 1.],
-                [10. 1.],
-                [20. 1.],
-                [30. 1.],
-                [40. 1.],
-                [50. 1.],
-                [60. 1.],
-                [70. 1.],
-                [80. 1.],
-                [90. 1.],
-                [100. 1.])
-
-mat = nanoconc.loadmaterial("Gold",disp=false)
-predict(x) = nanoconc.abspredict(1.333,250.,900.,0x00001000,x,mat,1000.,1.)
-spectra = predict.(particledata)
-
-for spectrum in spectra
-    plot(spectrum[:,1],spectrum[:,2])
-end
-show()

0-100test.jl

@@ -1,39 +0,0 @@
-println("\nImporting modules...")
-
-include("nanoconc.jl")
-using PyPlot
-using JLD2
-
-println("Loading parameters...")
-
-particledata = ([2.5 1.],
-                [5. 1.],
-                [10. 1.],
-                [20. 1.],
-                [30. 1.],
-                [40. 1.],
-                [50. 1.],
-                [60. 1.],
-                [70. 1.],
-                [80. 1.],
-                [90. 1.],
-                [100. 1.])
-
-mat = nanoconc.loadmaterial("Gold",disp=false)
-predict(x) = nanoconc.qpredict(1.333,250.,900.,0x00001000,x,mat)
-println("Calculating spectra...")
-print("Calculation time: ")
-
-@time spectra = predict.(particledata)
-
-println("Saving output...")
-
-println("Plotting spectra...")
-
-for spectrum in spectra
-    plot(spectrum[:,1],spectrum[:,2])
-end
-println("Displaying spectra...")
-println("Script complete!")
-show()
-println()

20nm.jl

@@ -1,28 +0,0 @@
-println("\nImporting modules...")
-
-include("nanoconc.jl")
-using PyPlot
-
-println("Loading parameters...")
-
-particledata = [20. 1.]
-
-mat = nanoconc.loadmaterial("Gold",disp=false)
-predict(x) = nanoconc.abspredict(1.333,450.,650.,0x00001000,x,mat,1000.,1.)
-
-println("Calculating spectra...")
-print("Calculation time: ")
-
-@time spectrum = predict(particledata)
-
-println("Finding lambda max...")
-#println("\nDebug data:\nfindmax = $(findmax(spectrum[:,2]))\nmaxind = $(findmax(spectrum[:,2])[2])")
-lmax = spectrum[findmax(spectrum[:,2])[2],1]
-println("lambda max = $(lmax)")
-
-println("Plotting spectra...")
-
-plot(spectrum[:,1],spectrum[:,2])
-println("Displaying spectra...")
-show()
-println("Script complete!")

abstest.jl

@@ -1,37 +0,0 @@
-println("\nImporting modules...")
-
-include("src/nanoconc.jl")
-using CSV
-using DataFrames
-using Profile, ProfileVega
-
-println("Loading parameters...")
-
-refmed = 1.333 # refractive index of the medium
-wavel1, wavel2 = 250., 900. # wavelengths to calculate between
-numval = 0x00001000 # number of values to calculate in spectrum
-particledata = [2.5 1.;
-                 5. 1.;
-                 10. 1.;
-                 20. 1.;
-                 30. 1.;
-                 40. 1.;
-                 50. 1.;
-                 60. 1.;
-                 70. 1.;
-                 80. 1.;
-                 90. 1.;
-                 100. 1.]
-materialdata = nanoconc.loadmaterial("Gold",disp=false)
-ppml = 10000. # particles per ml nanoconc.quantumcalc.numtomol(ppml) -> conc
-d0 = 1. # path length
-params = (refmed,wavel1,wavel2,numval,particledata,materialdata,ppml,d0)
-spectrum = nanoconc.abspredict(params...)
-
-println("Calculating absorbance spectrum...")
-print("Calculation time: ")
-
-@time spectrum = nanoconc.abspredict(params...)
-CSV.write("abs.csv", DataFrame(spectrum, :auto), writeheader=false)
-
-# @profview nanoconc.abspredict(params...)

bhmielibs_test.jl

@@ -0,0 +1,80 @@
+run(`scripts/build_other_impls.sh`)
+
+include("src/miemfp.jl")
+# using miemfp
+
+function bhmie_c(x::Float32, cxref::ComplexF32, nang::UInt32, cxs1::Vector{ComplexF32}, cxs2::Vector{ComplexF32})
+    # Pre-allocate memory for the output variables
+    qext = Ref{Float32}(0.0)
+    qsca = Ref{Float32}(0.0)
+    qback = Ref{Float32}(0.0)
+    gsca = Ref{Float32}(0.0)
+
+    # Ensure cxs1 and cxs2 have proper sizes, as expected by the C function
+    # For example, if they need to be of size `nang`, you should verify or resize them accordingly
+
+    # Call the C function
+    ccall((:bhmie, ".bhmielibs/bhmie-c/bhmie.so"), Cvoid,
+        (Float32, ComplexF32, UInt32, Ptr{ComplexF32}, Ptr{ComplexF32}, Ref{Float32}, Ref{Float32}, Ref{Float32}, Ref{Float32}),
+        x, cxref, nang, cxs1, cxs2, qext, qsca, qback, gsca)
+
+    # Return the output variables
+    return qext[], qsca[], qback[], gsca[]
+end
+
+function bhmie_fortran(x::Float32, refrel::ComplexF32, nang::Int32, s1::Vector{ComplexF32}, s2::Vector{ComplexF32})
+    # Pre-allocate output variables
+    qext = Ref{Float32}(0.0)
+    qsca = Ref{Float32}(0.0)
+    qback = Ref{Float32}(0.0)
+    gsca = Ref{Float32}(0.0)
+
+    # Call the Fortran subroutine
+    ccall((:bhmie_, ".bhmielibs/bhmie-f/bhmie.so"), Cvoid,
+          (Ref{Float32}, Ref{ComplexF32}, Ref{Int32}, Ptr{ComplexF32}, Ptr{ComplexF32}, Ref{Float32}, Ref{Float32}, Ref{Float32}, Ref{Float32}),
+          x, refrel, nang, s1, s2, qext, qsca, qback, gsca)
+
+    # Return the modified values
+    return qext[], qsca[], qback[], gsca[]
+end
+
+function bhmie_fortran77(x::Float32, refrel::ComplexF32, nang::Int32, s1::Vector{ComplexF32}, s2::Vector{ComplexF32})
+    # Pre-allocate output variables
+    qext = Ref{Float32}(0.0)
+    qsca = Ref{Float32}(0.0)
+    qback = Ref{Float32}(0.0)
+    gsca = Ref{Float32}(0.0)
+
+    # Call the Fortran subroutine
+    ccall((:bhmie_, ".bhmielibs/bhmie-f/bhmie.so"), Cvoid,
+          (Ref{Float32}, Ref{ComplexF32}, Ref{Int32}, Ptr{ComplexF32}, Ptr{ComplexF32}, Ref{Float32}, Ref{Float32}, Ref{Float32}, Ref{Float32}),
+          x, refrel, nang, s1, s2, qext, qsca, qback, gsca)
+
+    # Return the modified values
+    return qext[], qsca[], qback[], gsca[]
+end
+
+# Create test data
+x = Float32(1.0)  # Example value for x
+cxref = ComplexF32(1.5, 0.5)  # Example complex refractive index
+nang = UInt32(2)  # Example number of angles
+
+# Example arrays for scattering amplitudes, initialized with dummy complex values
+cxs1 = [ComplexF32(0.1, 0.2) for _ in 1:nang]
+cxs2 = [ComplexF32(0.3, 0.4) for _ in 1:nang]
+
+# Test C wrapper
+qext, qsca, qback, gsca = bhmie_c(x, cxref, nang, cxs1, cxs2)
+println("bhmie_c output: qext = $qext, qsca = $qsca, qback = $qback, gsca = $gsca")
+
+# Test Fortran wrapper
+qext, qsca, qback, gsca = bhmie_fortran(x, cxref, Int32(nang), cxs1, cxs2)
+println("bhmie_fortran output: qext = $qext, qsca = $qsca, qback = $qback, gsca = $gsca")
+
+# Test Fortran77 wrapper
+qext, qsca, qback, gsca = bhmie_fortran77(x, cxref, Int32(nang), cxs1, cxs2)
+println("bhmie_fortran77 output: qext = $qext, qsca = $qsca, qback = $qback, gsca = $gsca")
+
+# Test Julia wrapper
+qext, qsca, qback, gsca = miemfp.bhmie(Float64(x), ComplexF64(cxref), nang)
+println("bhmie_julia output: qext = $qext, qsca = $qsca, qback = $qback, gsca = $gsca")

scripts/build_other_impls.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+# This bash script will pull and compile the other implementations of the
+# bhmie algorithm (found at http://scatterlib.wikidot.com/mie)
+# These implementations will then be tested and benchmarked against the local
+# implementation to ensure that they are correct and (ideally) faster.
+
+# First, let's create a base URL for the scatterlib wiki codebases
+base_url="http://scatterlib.wikidot.com/local--files/codes/"
+
+# Next, let's create a list of the codebases we want to pull
+codebases=("bhmie-f.zip" "bhmie-c.zip")
+
+# Then, let's create a directory to pull the codebases to
+bhmie_dir=".bhmielibs"
+mkdir -p $bhmie_dir
+
+# Now, let's pull the codebases
+for codebase in ${codebases[@]}; do
+    wget -O $bhmie_dir/$codebase $base_url/$codebase
+    if [[ $codebase == *.zip ]]; then
+        unzip $bhmie_dir/$codebase -d $bhmie_dir/$codebase
+    fi
+done
+
+# Then, let's extract any .zip files to a directory of the same name (without the .zip, obviously)
+for codebase in ${codebases[@]}; do
+    if [[ $codebase == *.zip ]]; then
+        unzip $bhmie_dir/$codebase -d $bhmie_dir/${codebase%.zip}
+    fi
+done
+
+# If the folder already existed in the archive, move that folder one level up
+# and remove the now empty folder
+for codebase in ${codebases[@]}; do
+    if [[ $codebase == *.zip ]]; then
+        folder=${codebase%.zip}
+        if [ -d $bhmie_dir/$folder/$folder ]; then
+            mv $bhmie_dir/$folder/$folder/* $bhmie_dir/$folder
+            rmdir $bhmie_dir/$folder/$folder
+        fi
+    fi
+done
+
+# Next, if this has all succeeded we can delete the .zip files
+for codebase in ${codebases[@]}; do
+    if [[ $codebase == *.zip ]]; then
+        rm $bhmie_dir/$codebase
+    fi
+done
+
+# And, finally, we can compile the C, and Fortran implementations
+cd $bhmie_dir
+gcc -shared -fPIC -o bhmie-c/bhmie.so bhmie-c/bhmie.c bhmie-c/complex.c bhmie-c/nrutil.c -lm -Wno-builtin-declaration-mismatch -Wno-implicit-function-declaration
+gfortran -shared -fPIC -o bhmie-f/bhmie.so bhmie-f/bhmie.f
+gfortran -shared -fPIC -o bhmie-f/bhmie_f77.so bhmie-f/bhmie_f77.f

val_data/uv-vis/.~lock.UV VIS_Rasodyne _1.xlsx#

@@ -1 +0,0 @@
-Cian Hughes,cianh,cian-worklaptop,04.07.2023 11:49,file:///home/cianh/.config/libreoffice/4;

val_data/uv-vis/Ag_17092021/.~lock.AG1.xlsx#

@@ -1 +0,0 @@
-Cian Hughes,cianh,cian-worklaptop,04.07.2023 14:52,file:///home/cianh/.config/libreoffice/4;