From b2a305b5955431f924ee1ecc792419e4458ec896 Mon Sep 17 00:00:00 2001
From: baptiste <auguieba@gmail.com>
Date: Mon, 21 Nov 2022 21:48:27 +1300
Subject: [PATCH] fixed

---
 dev/book/dimer_linear.jl | 14 ++++++++++----
 src/Clusters.jl          |  8 ++++----
 src/HighLevel.jl         |  4 ++--
 src/Materials.jl         |  2 +-
 4 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/dev/book/dimer_linear.jl b/dev/book/dimer_linear.jl
index b8f5734..355c3e5 100644
--- a/dev/book/dimer_linear.jl
+++ b/dev/book/dimer_linear.jl
@@ -10,6 +10,8 @@ using FastGaussQuadrature
 using DataFrames
 using VegaLite
 
+using AlgebraOfGraphics, CairoMakie
+
 
 
 # dimer_model <- function(d, orientation = c("head-to-tail", "side-by-side"), 
@@ -95,10 +97,16 @@ wavelength = collect(450:2:850.0)
 media = Dict([("Au", epsilon_Au), ("medium", x -> 1.33)])
 mat = Material(wavelength, media)
 
+sizes = [SVector(0.0, 0.0, 0.0)]
+positions = [SVector(0.0, 0.0, 0.0)]
+# input parameters are Euler angles
+rotations = [UnitQuaternion(RotZYZ(0.0, 0.0, 0.0))]
+Cluster(positions, rotations, sizes, ["Au"], "particle")
+
 cl0 = cluster_single(20.0, 50.0, 20.0)
 # cl0 = cluster_single(50.0, 20.0, 20.0)
-# s = spectrum_dispersion(cl0, mat, [UnitQuaternion(RotZ(0.0))])
-s = spectrum_dispersion(cl0, mat, [SVector(0.0, 0.0, 0.0)])
+
+s = spectrum_dispersion(cl0, mat, [UnitQuaternion(RotZ(0.0))])
 single = dispersion_df(s, mat.wavelengths)
 
 
@@ -119,8 +127,6 @@ draw(layer * xy, facet=(; linkyaxes=:none))
 #     encoding = {x = "wavelength:q", y = "value:q", color = "d:n", strokeDash = "cluster:n"}
 # )
 
-using AlgebraOfGraphics, CairoMakie
-
 # set_aog_theme!()
 
 
diff --git a/src/Clusters.jl b/src/Clusters.jl
index 2b501c1..5ab3548 100644
--- a/src/Clusters.jl
+++ b/src/Clusters.jl
@@ -49,7 +49,7 @@ function cluster_single(a, b, c, α=0.0, β=0.0, γ=0.0, material="Au", type="pa
     sizes = [SVector(a, b, c)]
     positions = [SVector(0.0, 0.0, 0.0)]
     # input parameters are Euler angles
-    rotations = [UnitQuaternion(RotZYZ([α, β, γ]))]
+    rotations = [Rotations.UnitQuaternion(Rotations.RotZYZ(α, β, γ))]
     Cluster(positions, rotations, sizes, [material], type)
 end
 
@@ -159,7 +159,7 @@ cluster_line(3, 500, 20, 20, 30, 0, 0, 0)
 function cluster_line(N, Λ, a, b, c, α=0.0, β=0.0, γ=0.0, material="Au", type="particle")
 
     sizes = [SVector(a, b, c) for ii in 1:N] # identical particles
-    rotations = [UnitQuaternion(RotZYZ([α, β, γ])) for _ ∈ 1:N] # identical particles
+    rotations = [UnitQuaternion(RotZYZ(α, β, γ)) for _ ∈ 1:N] # identical particles
 
     positions = SVector.(-(N - 1)*Λ/2:Λ:(N-1)*Λ/2, zero(eltype(Λ)), zero(eltype(Λ)))
 
@@ -192,7 +192,7 @@ function cluster_array(N, Λ, a, b, c, α=0.0, β=0.0, γ=0.0, material="Au", ty
     N = N′^2 # actual number,  may have fewer than original N particles
 
     sizes = [SVector(a, b, c) for _ ∈ 1:N] # identical particles
-    rotations = [UnitQuaternion(RotZYZ([α, β, γ])) for _ ∈ 1:N] # identical particles
+    rotations = [UnitQuaternion(RotZYZ(α, β, γ)) for _ ∈ 1:N] # identical particles
 
     x = -(N′ - 1)*Λ/2:Λ:(N′-1)*Λ/2
     positions = SVector.(Iterators.product(x, x, zero(eltype(x))))[:]
@@ -245,7 +245,7 @@ function cluster_shell(N, a, b, c, R; orientation="radial", material="Rhodamine"
 
     end
 
-    quaternions = [UnitQuaternion(RotZYZ([r[1], r[2], r[3]])) for r in rotations]
+    quaternions = [UnitQuaternion(RotZYZ(r[1], r[2], r[3])) for r in rotations]
 
     Cluster(positions, inv.(quaternions), sizes, [material for _ ∈ 1:N], type)
 
diff --git a/src/HighLevel.jl b/src/HighLevel.jl
index 4e00a44..a3864b2 100644
--- a/src/HighLevel.jl
+++ b/src/HighLevel.jl
@@ -54,8 +54,8 @@ function spectrum_dispersion(
     # store all rotation matrices
     # ParticleRotations = map(euler_passive, cl.angles)
     ParticleRotations = map(RotMatrix, cl.rotations) # now (active) Rotation objects
-    IncidenceRotations = map(euler_active, Incidence) # old Euler, no longer needed
-    #IncidenceRotations = map(RotMatrix, Incidence) # now given as quaternions
+    # IncidenceRotations = map(euler_active, Incidence) # old Euler, no longer needed
+    IncidenceRotations = map(RotMatrix, Incidence) # now given as quaternions
     ScatteringVectors = map(euler_unitvector, quad_sca.nodes)
     # NOTE: we only need the third column to rotate kz, should specialise
 
diff --git a/src/Materials.jl b/src/Materials.jl
index 8e068f5..4d438ad 100644
--- a/src/Materials.jl
+++ b/src/Materials.jl
@@ -265,7 +265,7 @@ function alpha_kuwata(λ, ε, ε_m, Size)
 
     V = 4π / 3 * prod(Size)
     x = @. 2π / λ * Size
-    χ = depolarisation_spheroid(Size...)
+    χ = depolarisation_ellipsoid(Size...)
 
     A = @. -0.4865 * χ - 1.046 * χ^2 + 0.8481 * χ^3
     B = @. 0.01909 * χ + 0.19999 * χ^2 + 0.6077 * χ^3