Merge pull request #17 from bblankrot/dev

Last PR before 0.0.2
bblankrot · Apr 16, 2018 · 7f555f8 · 7f555f8
2 parents b576f2d + d6056be
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# ParticleScattering.jl
+# ParticleScattering
 
 [![Travis](https://travis-ci.org/bblankrot/ParticleScattering.jl.svg?branch=master)](https://travis-ci.org/bblankrot/ParticleScattering.jl)
 [![AppVeyor](https://ci.appveyor.com/api/projects/status/p0p636vtrx95ch8m/branch/master?svg=true)](https://ci.appveyor.com/project/bblankrot/particlescattering-jl/branch/master)
@@ -11,11 +11,16 @@ those containing a large number of penetrable smooth
 particles. Provides the ability to optimize over the
 particle parameters for various design problems.
 
-# Installation
+### Installation
 
-Currently, only Julia 0.6 is supported, and the package must be installed
-manually. See directions at [the official Julia documentation](https://docs.julialang.org/en/stable/manual/packages/#Installing-Unregistered-Packages-1).
+ParticleScattering can be installed using `Pkg.add`. Currently, only Julia 0.6 is supported.
+
+```julia
+Pkg.add("ParticleScattering")
+using ParticleScattering
+```
 
 ### Community
 
-The easiest way to contribute is by opening issues! Of course, we'd be more than happy if you implement any fixes and send a PR. If you have any relevant scattering problems that would make good examples for the docs, feel free to open an issue for that as well.
+The easiest way to contribute is by opening issues! Of course, we'd be more than happy if you implement any fixes and send a PR.
+If you have any relevant scattering problems that would make good examples for the docs, feel free to open an issue for that as well.
diff --git a/REQUIRE b/REQUIRE
@@ -6,4 +6,4 @@ Optim 0.14.0
 PyPlot
 DataFrames
 CSV
-PGFPlotsX
+PGFPlotsX 0.2.1
diff --git a/docs/make.jl b/docs/make.jl
@@ -13,6 +13,7 @@ makedocs(format = :html,
             "tutorial_optim_radius.md"
         ],
         "Choosing Minimal N and P" => "minimalNP.md",
+        "Adding New Shapes" => "new_shapes.md",
         "API" => "api.md"
     ]
 )

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -7,9 +7,10 @@ particles. Provides the ability to optimize over particle parameters for various
 
 ## Installation
 
-Currently, only Julia 0.6 is supported. Once Julia is set up, ParticleScattering can be installed by running
+ParticleScattering can be installed using `Pkg.add`. Currently, only Julia 0.6 is supported.
+
 ```julia
-Pkg.clone(https://github.com/bblankrot/ParticleScattering.jl.git)
+Pkg.add("ParticleScattering")
 using ParticleScattering
 ```
 which also installs the following dependencies:

diff --git a/docs/src/new_shapes.md b/docs/src/new_shapes.md
@@ -0,0 +1,17 @@
+# Adding New Shapes
+
+ParticleScattering includes functions for drawing squircles, rounded stars, and ellipses.
+New shape functions can  be added, provided they have the following structure:
+```julia
+function my_shape(args, N)
+    t = Float64[π*j/N for j = 0:(2*N-1)] # or t = 0:π/N:π*(2-1/N)
+    ft =  [x    y]
+    dft = [dx/dt    dy/dt]
+    ShapeParams(t, ft, dft)
+end
+```
+
+Where `t` is the parametrization variable, `ft[i,:] = [x(t[i]) y(t[i])]` contains the coordinates, and dft contains the derivative of `ft` with respect to `t`.
+In particular, the quadrature used by ParticleScattering assumes `t`
+are equidistantly distributed in ``[0, 2\pi)``, and that none of the points `ft`
+lie on the origin.
diff --git a/examples/sim0_min_NP.jl b/examples/sim0_min_NP.jl
@@ -121,20 +121,16 @@ JLD.@load dirname(@__FILE__) * "/mindata_5_new.jld"
 JLD.@load dirname(@__FILE__) * "/mindata_s_new.jld"
 
 pgf.@pgf begin
-    N_plot5 = pgf.Plot(pgf.Coordinates(errN5,N5),
-        {blue, dashdotdotted, no_markers, thick},
-		label = "\$N_{\\mathrm{min}} \\, \\mathrm{(star)}\$")
-    P_plot5 = pgf.Plot(pgf.Coordinates(errN5,P5),
-        {"green!50!black", no_markers, thick},
-		label = "\$P_{\\mathrm{min}} \\, \\mathrm{(star)}\$")
-    N_plot = pgf.Plot(pgf.Coordinates(errNs,Ns),
-        {red, dotted, no_markers, thick},
-		label = "\$N_{\\mathrm{min}} \\, \\mathrm{(squircle)}\$")
-    P_plot = pgf.Plot(pgf.Coordinates(errNs,Ps),
-        {black, dashed, no_markers, thick},
-		label = "\$P_{\\mathrm{min}} \\, \\mathrm{(squircle)}\$")
-    ax = pgf.Axis([N_plot5, N_plot, P_plot5, P_plot],
-        {
+    N_plot5 = pgf.Plot({blue, dashdotdotted, no_markers, thick},
+						pgf.Coordinates(errN5,N5))
+	N_plot = pgf.Plot({red, dotted, no_markers, thick},
+						pgf.Coordinates(errNs,Ns))
+	P_plot5 = pgf.Plot({"green!50!black", no_markers, thick},
+						pgf.Coordinates(errN5,P5))
+    P_plot = pgf.Plot({black, dashed, no_markers, thick},
+						pgf.Coordinates(errNs,Ps))
+    ax = pgf.Axis(
+    	{
             xmin = 5e-10,
             xmax = 1e-1,
 			xlabel = "\$\\Delta u\$",
@@ -144,17 +140,22 @@ pgf.@pgf begin
             legend_pos = "north east",
             legend_style = "font = \\footnotesize",
 			legend_cell_align = "left"
-        })
+        },
+		[N_plot5, N_plot, P_plot5, P_plot],
+		pgf.Legend(["\$N_{\\mathrm{min}} \\, \\mathrm{(star)}\$",
+					"\$N_{\\mathrm{min}} \\, \\mathrm{(squircle)}\$",
+					"\$P_{\\mathrm{min}} \\, \\mathrm{(star)}\$",
+					"\$P_{\\mathrm{min}} \\, \\mathrm{(squircle)}\$"]))
+
 end
 pgf.save(dirname(@__FILE__) * "/tikz/minNP.tex", ax ,include_preamble = false)
 
 shape = myshapefun5(200)
 pgf_shape = pgf.Coordinates([shape.ft[:,1];shape.ft[1,1]],
                             [shape.ft[:,2];shape.ft[1,2]])
 pgf.@pgf begin
-    ax2 = pgf.Axis(pgf.Plot(pgf_shape, {thick, black, no_markers, fill = "black!20"}),
-        {   axis_equal,
-            ticks = "none"})
+    ax2 = pgf.Axis({axis_equal, ticks = "none"}, pgf.Plot({thick, black,
+			no_markers, fill = "black!20"}, pgf_shape))
     Rd = shape.R
     push!(ax2, "\\addplot [black, dashed, thick, domain=0:2*pi,samples=100]({$(shape.R)*cos(deg(x))},{$(shape.R)*sin(deg(x))});")
     push!(ax2, "\\node at (axis cs: -0.28,-0.15) {\$D\$};")
@@ -169,10 +170,9 @@ shape = myshapefun_squircle(200)
 pgf_shape = pgf.Coordinates([shape.ft[:,1];shape.ft[1,1]],
                             [shape.ft[:,2];shape.ft[1,2]])
 pgf.@pgf begin
-    ax3 = pgf.Axis(pgf.Plot(pgf_shape, {thick, black, no_markers, fill = "black!20"}),
-        {   axis_equal,
-            ticks = "none"})
-    Rd = shape.R
+	ax3 = pgf.Axis({axis_equal, ticks = "none"}, pgf.Plot({thick, black,
+					no_markers, fill = "black!20", label="bla"}, pgf_shape))
+	Rd = shape.R
     push!(ax3, "\\addplot [black, dashed, thick, domain=0:2*pi,samples=100]({$(shape.R)*cos(deg(x))},{$(shape.R)*sin(deg(x))});")
     push!(ax3, "\\node at (axis cs: -0.28,-0.15) {\$D\$};")
     push!(ax3, "\\node at (axis cs: 0.25,-0.25) {\$k_0\$};")

diff --git a/examples/sim1_complexity.jl b/examples/sim1_complexity.jl
@@ -39,7 +39,6 @@ for i=1:simlen-1
 end
 dt0 /= simlen
 
-
 for is = 1:simlen, it = 1:trials
     #compute shape variables
     begin #setup
@@ -123,27 +122,27 @@ pgf.@pgf begin
             ylabel = "\$ \\mathrm{Run time} \\ [\\mathrm{s}]\$",
             xmode = "linear",
             ymode = "log",
-            width = "\\figurewidth",
+            width = "10cm",
             legend_pos = "north west",
-            legend_style = "font = \\footnotesize"})
-    push!(ax, pgf.Plot(pgf.Coordinates(M_vec, res_vec),
-            {blue, "only marks", mark = "*"};
-            label = "Elapsed time (solution)"))
-            temp2 = floor(log10(10^a_total))
-            temp1 = 10^a_total/10^temp2
-    push!(ax, pgf.Plot(pgf.Coordinates(M_vec, res_ana),
-            {blue, thick, no_markers};
-            label = @sprintf("\$%.1f \\cdot 10^{%d} \\cdot M^{%.2f}\$",
-                temp1, temp2, b_total)))
-    push!(ax, pgf.Plot(pgf.Coordinates(M_vec, mvp_vec),
-            {red, only_marks, mark = "triangle*", mark_options = {fill = "red"}};
-            label= "Elapsed time (MVP)"))
-            temp2 = floor(log10(10^a_mvp))
-            temp1 = 10^a_mvp/10^temp2
-    push!(ax, pgf.Plot(pgf.Coordinates(M_vec, mvp_ana),
-            {red, thick, dashed, no_markers};
-            label = @sprintf("\$%.1f \\cdot 10^{%d} \\cdot M^{%.2f}\$",
-                temp1, temp2, b_mvp)))
+            legend_style = "font = \\footnotesize",
+            legend_cell_align = "left"})
+    push!(ax, pgf.Plot({blue, "only marks", mark = "*"},
+                        pgf.Coordinates(M_vec, res_vec)))
+    tmp_total = floor(log10(10^a_total))
+    push!(ax, pgf.Plot({blue, thick, no_markers},
+                        pgf.Coordinates(M_vec, res_ana)))
+    push!(ax, pgf.Plot({red, only_marks, mark = "triangle*",
+                        mark_options = {fill = "red"}},
+                        pgf.Coordinates(M_vec, mvp_vec)))
+    tmp_mvp = floor(log10(10^a_mvp))
+    push!(ax, pgf.Plot({red, thick, dashed, no_markers},
+                        pgf.Coordinates(M_vec, mvp_ana)))
+    push!(ax, pgf.Legend([
+                    "Elapsed time (solution)",
+                    @sprintf("\$%.1f \\cdot 10^{%d} \\cdot M^{%.2f}\$",
+                            10^a_total/10^tmp_total, tmp_total, b_total),
+                    "Elapsed time (MVP)",
+                    @sprintf("\$%.1f \\cdot 10^{%d} \\cdot M^{%.2f}\$",
+                            10^a_mvp/10^tmp_mvp, tmp_mvp, b_mvp)]))
 end
-
 pgf.save(dirname(@__FILE__) * "/sim1.tex", ax ,include_preamble = false)
diff --git a/examples/sim2_LuneburgOptim.jl b/examples/sim2_LuneburgOptim.jl
@@ -45,21 +45,21 @@ sp1 = ScatteringProblem([CircleParams(rs_lnbrg[i]) for i in eachindex(rs_lnbrg)]
         ids_lnbrg, centers, φs)
 Ez1 = plot_near_field(k0, kin, P, sp1, θ_i, x_points = 150, y_points = 150,
         opt = fmm_options, border = border)
-plotNearField_pgf(filename1, k0, kin, P, sp1, θ_i; opt = fmm_options,
+plot_near_field_pgf(filename1, k0, kin, P, sp1, θ_i; opt = fmm_options,
     x_points = 201, y_points = 201, border = border)
 
 sp2 = ScatteringProblem([CircleParams(rs_max[i]) for i in eachindex(rs_max)],
         ids_max, centers, φs)
 Ez2 = plot_near_field(k0, kin, P, sp2, θ_i, x_points = 150, y_points = 150,
             opt = fmm_options, border = border)
-plotNearField_pgf(filename2, k0, kin, P, sp2, θ_i; opt = fmm_options,
+plot_near_field_pgf(filename2, k0, kin, P, sp2, θ_i; opt = fmm_options,
     x_points = 201, y_points = 201, border = border)
 
 sp3 = ScatteringProblem([CircleParams(rs0[i]) for i in eachindex(rs0)],
         collect(1:length(rs0)), centers, φs)
 Ez3 = plot_near_field(k0, kin, P, sp3, θ_i, x_points = 150, y_points = 150,
         opt = fmm_options, border = border)
-plotNearField_pgf(filename3, k0, kin, P, sp3, θ_i; opt = fmm_options,
+plot_near_field_pgf(filename3, k0, kin, P, sp3, θ_i; opt = fmm_options,
     x_points = 201, y_points = 201, border = border)
 
 #plot convergence
@@ -81,23 +81,26 @@ JLD.@save output_dir * "/luneburg_optim.jld"
 
 import PGFPlotsX; const pgf = PGFPlotsX
 pgf.@pgf begin
-    fobj_plot = pgf.Plot(pgf.Coordinates(0:inner_iters-1, fobj),
-                {blue, thick, no_markers},
-                label = "\$f_{\\mathrm{obj}}\$")
-    gobj_plot = pgf.Plot(pgf.Coordinates(0:inner_iters-1, gobj),
-                {red, thick, dashed, no_markers},
-                label = "\$\\|\\mathbf{g}_{\\mathrm{obj}}\\|_{\\infty}\$")
-    fobj_outer = pgf.Plot(pgf.Coordinates((0:inner_iters-1)[rng], fobj[rng]),
-                {blue, only_marks, mark = "*", mark_options = {fill = "blue"}})
-    gobj_outer = pgf.Plot(pgf.Coordinates((0:inner_iters-1)[rng], gobj[rng]),
-                {red, only_marks, mark = "triangle*", mark_options = {fill = "red"}})
-    ax = pgf.Axis([fobj_plot;gobj_plot;fobj_outer;gobj_outer],
-        {
-            width = "\\figurewidth",
-            xlabel = "Iterations",
-            legend_pos = "north east",
-            legend_style = "font = \\footnotesize"
-        })
+    fobj_plot = pgf.Plot({blue, thick, no_markers},
+                        pgf.Coordinates(0:inner_iters-1, fobj))
+    gobj_plot = pgf.Plot({red, thick, dashed, no_markers},
+                        pgf.Coordinates(0:inner_iters-1, gobj))
+    fobj_outer = pgf.Plot({blue, only_marks, mark = "*",
+                            mark_options = {fill = "blue"}},
+                        pgf.Coordinates((0:inner_iters-1)[rng], fobj[rng]))
+    gobj_outer = pgf.Plot({red, only_marks, mark = "triangle*",
+                            mark_options = {fill = "red"}},
+                        pgf.Coordinates((0:inner_iters-1)[rng], gobj[rng]))
+    ax = pgf.Axis({ xmin = 0,
+                    width = "6cm",
+                    xlabel = "Iterations",
+                    legend_pos = "north east",
+                    legend_style = "font = \\footnotesize",
+                    legend_cell_align = "left"},
+                fobj_plot, gobj_plot, fobj_outer, gobj_outer)
+    push!(ax, pgf.Legend(["\$f_{\\mathrm{obj}}\$";
+                        "\$\\|\\mathbf{g}_{\\mathrm{obj}}\\|_{\\infty}\$"]))
+    ax
 end
 pgf.save(output_dir * "/opt_r_conv.tex", ax ,include_preamble = false)
 

diff --git a/examples/sim3_AngleOpt.jl b/examples/sim3_AngleOpt.jl
@@ -74,18 +74,18 @@ plot_near_field(k0, kin, P, sp_before, θ_i,
                 x_points = 600, y_points = 200, border = plot_border);
 colorbar()
 clim([0;5])
-plotNearField_pgf(output_dir * "/opt_phi_before.tex", k0, kin, P,
-    sp_before, θ_i; opt = fmm_options, x_points = 600, y_points = 200,
-    border = plot_border, downsample = 4)
+plot_near_field_pgf(output_dir * "/opt_phi_before.tex", k0, kin, P,
+    sp_before, θ_i; opt = fmm_options, x_points = 150, y_points = 50,
+    border = plot_border, downsample = 10, include_preamble = true)
 
 sp_after = ScatteringProblem(shapes, ids, centers, test_max.minimizer)
 plot_near_field(k0, kin, P, sp_after, θ_i,
                 x_points = 600, y_points = 200, border = plot_border)
 colorbar()
 clim([0;5])
-plotNearField_pgf(output_dir * "/opt_phi_after.tex", k0, kin, P,
-    sp_after, θ_i; opt = fmm_options, x_points = 600, y_points = 200,
-    border = plot_border, downsample = 4)
+plot_near_field_pgf(output_dir * "/opt_phi_after.tex", k0, kin, P,
+    sp_after, θ_i; opt = fmm_options, x_points = 150, y_points = 50,
+    border = plot_border, downsample = 10, include_preamble = true)
 
 inner_iters = length(test_max.trace)
 fobj = -[test_max.trace[i].value for i=1:inner_iters]
@@ -95,20 +95,17 @@ figure()
 plot(0:inner_iters-1, fobj)
 plot(0:inner_iters-1, gobj)
 
-import PGFPlotsX; const pgf = PGFPlotsX
 pgf.@pgf begin
-    fobj_plot = pgf.Plot(pgf.Coordinates(0:inner_iters-1, fobj),
-                {blue, thick, no_markers},
-                label = "\$f_{\\mathrm{obj}}\$")
-    gobj_plot = pgf.Plot(pgf.Coordinates(0:inner_iters-1, gobj),
-                {red, thick, dashed, no_markers},
-                label = "\$\\|\\mathbf{g}_{\\mathrm{obj}}\\|\$")
-    ax = pgf.Axis([fobj_plot;gobj_plot],
-        {
-            width = "\\figurewidth",
-            xlabel = "Iterations",
-            legend_pos = "north east",
-            legend_style = "font = \\footnotesize"
-        })
+    fobj_plot = pgf.Plot({blue, thick, no_markers},
+                        pgf.Coordinates(0:inner_iters-1, fobj))
+    gobj_plot = pgf.Plot({red, thick, dashed, no_markers},
+                        pgf.Coordinates(0:inner_iters-1, gobj))
+    ax = pgf.Axis({ width = "6cm",
+                    xlabel = "Iterations",
+                    legend_pos = "north east",
+                    legend_style = "font = \\footnotesize"},
+                fobj_plot, gobj_plot)
+    push!(ax, pgf.Legend(["\$f_{\\mathrm{obj}}\$";
+                        "\$\\|\\mathbf{g}_{\\mathrm{obj}}\\|\$"]))
 end
 pgf.save(output_dir * "/opt_phi_conv.tex", ax ,include_preamble = false)
diff --git a/paper/fig.png b/paper/fig.png
diff --git a/paper/paper.bib b/paper/paper.bib
@@ -0,0 +1,32 @@
+@article{ar:blankrot2018,
+	author = {Boaz Blankrot and Clemens Heitzinger},
+	title = {Efficient computational design and optimization of dielectric metamaterial devices},
+	journal = {submitted for publication},
+	year = {2018}
+}
+
+@article{ar:optimjl,
+	doi = {10.21105/joss.00615},
+	url = {https://doi.org/10.21105/joss.00615},
+	year  = {2018},
+	month = {apr},
+	publisher = {The Open Journal},
+	volume = {3},
+	number = {24},
+	pages = {615},
+	author = {Patrick K Mogensen and Asbj{\o}rn N Riseth},
+	title = {Optim: A mathematical optimization package for Julia},
+	journal = {Journal of Open Source Software}
+}
+
+@article{ar:alldielectric,
+	title={All-dielectric metamaterials},
+	author={Jahani, Saman and Jacob, Zubin},
+	journal={Nature Nanotechnology},
+	volume={11},
+	number={1},
+	pages={23--36},
+	year={2016},
+	publisher={Nature Research},
+	doi={10.1038/nnano.2015.304}
+}