Implement vector graphics and adjust figure sizes

.github/scripts/fix-timestamps

@@ -0,0 +1,9 @@
+#!/usr/bin/env sh
+
+# This script fixes the timestamps of all files in the current git repository
+
+git ls-tree -r --name-only HEAD | while read filename; do
+  unixtime=$(git log -1 --format="%at" -- "${filename}")
+  touchtime=$(date -d @$unixtime +'%Y%m%d%H%M.%S')
+  touch -t ${touchtime} "${filename}"
+done

.github/workflows/preview.yml

@@ -29,14 +29,10 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
         with:
           precompile: true
-      - uses: cardinalby/export-env-action@v2
-        with:
-          envFile: '_environment'    
-          expand: 'true'
+      - name: Fix Timestamps
+        run: bash .github/scripts/fix-timestamps
       - name: Quarto Render
         uses: quarto-dev/quarto-actions/render@v2
-        with:
-          to: html
       - name: Deploy PR Preview
         uses: rossjrw/[email protected]
         with:

.github/workflows/publish.yml

@@ -7,7 +7,7 @@ on: # either one of the following three cases
     - cron: '0 0 * * 0' # weekly (every Sunday)
 
   push:
-    branches: main
+    branches: [main]
 
 jobs:
   build:
@@ -26,10 +26,8 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
         with:
           precompile: true
-      - uses: cardinalby/export-env-action@v2
-        with:
-          envFile: '_environment'    
-          expand: 'true'
+      - name: Fix Timestamps
+        run: bash .github/scripts/fix-timestamps
       - name: Quarto Render
         uses: quarto-dev/quarto-actions/render@v2
         with:

HierarchicalEOM.jl/SIAM.qmd

@@ -1,7 +1,9 @@
 ---
 title: "Single-impurity Anderson model"
 author: Yi-Te Huang
-date: 2025-05-22  # last update (keep this comment as a reminder)
+date: last-modified
+
+engine: julia
 ---
 
 ## Introduction
@@ -27,6 +29,8 @@ Now, we need to build the system Hamiltonian and initial state with the package
 ```{julia}
 using HierarchicalEOM  # this automatically loads `QuantumToolbox`
 using CairoMakie       # for plotting results
+
+CairoMakie.activate!(type = "svg")
 ```
 
 ```{julia}
@@ -88,7 +92,7 @@ dos = DensityOfStates(M_odd, ados_s, d_up, ωlist)
 plot the results
 
 ```{julia}
-fig = Figure(size = (500, 350))
+fig = Figure()
 ax = Axis(fig[1, 1], xlabel = L"\omega")
 lines!(ax, ωlist, dos)
 

HierarchicalEOM.jl/cavityQED.qmd

@@ -1,7 +1,9 @@
 ---
 title: "Cavity QED system"
 author: Shen-Liang Yang, Yi-Te Huang
-date: 2025-05-22  # last update (keep this comment as a reminder)
+date: last-modified
+
+engine: julia
 ---
 
 ## Introduction
@@ -41,6 +43,8 @@ Now, we need to build the system Hamiltonian and initial state with the package
 ```{julia}
 using HierarchicalEOM  # this automatically loads `QuantumToolbox`
 using CairoMakie       # for plotting results
+
+CairoMakie.activate!(type = "svg")
 ```
 
 ```{julia}
@@ -96,7 +100,7 @@ Ct = correlation_function(Bath, tlist_test);
 Ct2 = correlation_function(Bath_test, tlist_test)
 
 # plot
-fig = Figure(size = (500, 350))
+fig = Figure()
 ax = Axis(fig[1, 1], xlabel = L"t", ylabel = L"C(t)")
 lines!(ax, tlist_test, real(Ct2), label = L"$N=1000$ (real part)", linestyle = :solid)
 lines!(ax, tlist_test, real(Ct),  label = L"$N=20$ (real part)", linestyle = :dash)
@@ -154,7 +158,7 @@ np_steady_H = expect(a' * a, steady_H)
 plot results
 
 ```{julia}
-fig = Figure(size = (600, 350))
+fig = Figure()
 
 ax1 = Axis(fig[1, 1], xlabel = L"t")
 lines!(ax1, t_list, σz_evo_H, label = L"\langle \sigma_z \rangle", linestyle = :solid)
@@ -176,7 +180,7 @@ fig
 psd_H = PowerSpectrum(M_Heom, steady_H, a, ω_list)
 
 # plot
-fig = Figure(size = (500, 350))
+fig = Figure()
 ax = Axis(fig[1, 1], xlabel = L"\omega")
 lines!(ax, ω_list, psd_H)
 
@@ -223,7 +227,7 @@ np_steady_M = expect(a' * a, steady_M);
 plot results
 
 ```{julia}
-fig = Figure(size = (600, 350))
+fig = Figure()
 
 ax1 = Axis(fig[1, 1], xlabel = L"t")
 lines!(ax1, t_list, σz_evo_M, label = L"\langle \sigma_z \rangle", linestyle = :solid)

HierarchicalEOM.jl/dynamical_decoupling.qmd

@@ -1,7 +1,9 @@
 ---
 title: "Driven systems and dynamical decoupling"
 author: Yi-Te Huang
-date: 2025-05-22  # last update (keep this comment as a reminder)
+date: last-modified
+
+engine: julia
 ---
 
 Inspirations taken from an example in QuTiP-BoFiN article [@QuTiP-BoFiN2023].
@@ -37,6 +39,8 @@ Now, we need to build the system Hamiltonian and initial state with the package
 ```{julia}
 using HierarchicalEOM  # this automatically loads `QuantumToolbox`
 using CairoMakie       # for plotting results
+
+CairoMakie.activate!(type = "svg")
 ```
 
 ```{julia}
@@ -91,7 +95,7 @@ fastTuple = (V = amp_fast, Δ = delay)
 slowTuple = (V = amp_slow, Δ = delay)
 
 # plot
-fig = Figure(size = (600, 350))
+fig = Figure()
 ax = Axis(fig[1, 1], xlabel = L"t")
 lines!(ax, tlist, [pulse(fastTuple, t) for t in tlist], label = "Fast Pulse", linestyle = :solid)
 lines!(ax, tlist, [pulse(slowTuple, t) for t in tlist], label = "Slow Pulse", linestyle = :dash)
@@ -152,7 +156,7 @@ slowPulseSol = HEOMsolve(M, ψ0, tlist; e_ops = [ρ01], H_t = H_D, params = slow
 ## Plot the coherence
 
 ```{julia}
-fig = Figure(size = (600, 350))
+fig = Figure()
 ax = Axis(fig[1, 1], xlabel = L"t", ylabel = L"\rho_{01}")
 lines!(ax, tlist, real(fastPulseSol.expect[1, :]), label = "Fast Pulse", linestyle = :solid)
 lines!(ax, tlist, real(slowPulseSol.expect[1, :]), label = "Slow Pulse", linestyle = :dot)

HierarchicalEOM.jl/electronic_current.qmd

@@ -1,7 +1,9 @@
 ---
 title: "Electronic Current"
 author: Yi-Te Huang
-date: 2025-05-22  # last update (keep this comment as a reminder)
+date: last-modified
+
+engine: julia
 ---
 
 Inspirations taken from [qutip documentation](https://qutip.org/documentation.html).
@@ -28,6 +30,8 @@ Now, we need to build the system Hamiltonian and initial state with the package
 ```{julia}
 using HierarchicalEOM  # this automatically loads `QuantumToolbox`
 using CairoMakie       # for plotting results
+
+CairoMakie.activate!(type = "svg")
 ```
 
 ```{julia}
@@ -149,7 +153,7 @@ end
 plot the result
 
 ```{julia}
-fig = Figure(size = (500, 350))
+fig = Figure()
 ax = Axis(fig[1, 1], xlabel = "time", ylabel = "Current")
 lines!(ax, tlist, Ie_L, label = "Bath L", color = :blue, linestyle = :solid)
 lines!(ax, tlist, Ie_R, label = "Bath R", color = :red, linestyle = :solid)

QuantumToolbox.jl/time_evolution/Dicke.qmd

@@ -1,7 +1,9 @@
 ---
 title: "The Dicke Model"
 author: Li-Xun Cai
-date: 2025-05-22  # last update (keep this comment as a reminder)
+date: last-modified
+
+engine: julia
 ---
 
 Inspirations taken from [this QuTiP tutorial](https://nbviewer.org/urls/qutip.org/qutip-tutorials/tutorials-v5/lectures/Lecture-3A-Dicke-model.ipynb) by J. R. Johansson.
@@ -48,6 +50,8 @@ This formulation reduces complexity, as it allows us to work on a collective bas
 ```{julia}
 using QuantumToolbox
 using CairoMakie
+
+CairoMakie.activate!(type = "svg")
 ```
 
 ```{julia}
@@ -105,7 +109,7 @@ Jzvec = expect(Jz0, ψGs);
 ```
 
 ```{julia}
-fig = Figure(size = (800, 300))
+fig = Figure(size=(900, 350))
 axn = Axis(
  fig[1,1],
  xlabel = "interaction strength",
@@ -119,7 +123,7 @@ axJz = Axis(
 ylims!(-N0/2, N0/2)
 lines!(axn, gs, real(nvec))
 lines!(axJz, gs, real(Jzvec))
-display(fig);
+fig
 ```
 The expectation value of photon number and $\hat{J}_z$ showed a sudden increment around $g_c$. 
 
@@ -140,11 +144,12 @@ for (hpos, idx) in enumerate(cases)
 
     # plot fock distribution
     _, ax2 = plot_fock_distribution(ρcav, location = fig[2,hpos])
+
+    ax2.xticks = (0:2:size(ρcav,1)-1, string.(0:2:size(ρcav,1)-1))
 
     if hpos != 1
-        ax.xlabelvisible, ax.ylabelvisible, ax2.ylabelvisible = fill(false, 3)
-        ax.xticksvisible, ax.yticksvisible, ax2.yticksvisible = fill(false, 3)
-        ax2.yticks = (0:0.5:1, ["" for i in 0:0.5:1])
+        hideydecorations!(ax, ticks=false)
+        hideydecorations!(ax2, ticks=false)
         if hpos == 5 # Add colorbar with the last returned heatmap (_hm) 
             Colorbar(fig[1,6], hm)
         end
@@ -158,7 +163,7 @@ lines!(ax3, gs, real(nvec), color=:teal)
 ax3.xlabelsize, ax3.ylabelsize = 20, 20
 vlines!(ax3, gs[cases], color=:orange, linestyle = :dash, linewidth = 4)
 
-display(fig);
+fig
 ```
 As $g$ increases, the cavity ground state's wigner function plot looks more coherent than a thermal state.
 
@@ -174,7 +179,7 @@ end;
 ```
 
 ```{julia}
-fig = Figure(size=(800, 400))
+fig = Figure(size=(900, 400))
 ax = Axis(fig[1,1])
 ax.xlabel = "coupling strength"
 ax.ylabel = "mutual entropy"
@@ -184,7 +189,7 @@ for (idx, slist) in enumerate(slists)
 end
 
 Legend(fig[1,2], ax, label = "number of atoms")
-display(fig);
+fig
 ```
 We further consult mutual entropy between the cavity and the spins as a measure of their correlation; the result showed that as the number of atoms $N$ increases, the peak of mutual entropy moves closer to $g_c$.
 

QuantumToolbox.jl/time_evolution/adiabatic.qmd

@@ -1,7 +1,9 @@
 ---
 title: "Adiabatic sweep (with `QuantumObjectEvolution`)"
 author: Li-Xun Cai
-date: 2025-05-22  # last update (keep this comment as a reminder)
+date: last-modified
+
+engine: julia
 ---
 
 Inspirations taken from [the QuTiP tutorial](https://nbviewer.org/urls/qutip.org/qutip-tutorials/tutorials-v5/lectures/Lecture-8-Adiabatic-quantum-computing.ipynb) by J. R. Johansson.
@@ -40,6 +42,8 @@ where the parameter $T$ determines how slow the Hamiltonian changes in time.
 ```{julia}
 using QuantumToolbox
 using CairoMakie
+
+CairoMakie.activate!(type = "svg")
 ```
 
 ```{julia}
@@ -104,15 +108,15 @@ end
 ```
 
 ```{julia}
-fig = Figure(size=(800, 400))
+fig = Figure(size=(900, 400))
 ax = Axis(fig[1,1], xticks = (0:0.25:1, ["$(t)T" for t in 0:0.25:1]))
 
 for idx in 1:20 # only check for the lowest 20 eigenvalues
     color = (idx == 1) ? :magenta : (:gray,0.5)
     lines!(ax, range(0,1,length(tlist)), eigs[:,idx], label = string(idx), color = color)
 end
 
-display(fig)
+fig
 ```
 
 The plot shows that the gap is nonvanishing and thus validates the evolution. So we proceed to check the expectation value dynamics of the final Hamiltonian and the fidelity dynamics to the truthful ground state throughout the evolution.
@@ -127,7 +131,7 @@ end;
 ```
 
 ```{julia}
-fig = Figure(size=(800, 400))
+fig = Figure(size=(900, 400))
 axs = Axis.([fig[1,1], fig[1,2]])
 axs[1].title = L"\langle H_f \rangle"
 axs[1].xticks = (0:0.25:1, ["$(t)T" for t in 0:0.25:1])
@@ -143,7 +147,7 @@ end
 
 Legend(fig[1,3], axs[1], L"T")
 
-display(fig)
+fig
 ```
 As the plot showed, the fidelity between the prepared final state and the truthful ground state reaches 1 as the total evolution time $T$ increases, showcasing the requirement of the adiabatic theorem that the change has to be gradual.