VegaLite support for non-periodic fields

[pablosanjose]

Closes #151

This implements the proposal in #151, on top of the PR #150. Together, these allow to plot Greens functions and other fields on unbounded lattices.

As an example we plot the (square of the) local density of states at ω = 0.01 of a semi-infinite (x>0) zigzag graphene nanoribbon, which is not uniform since the boundary creates a standing wave close to the two zigzag edges.

julia> using VegaLite, ProgressMeter, LinearAlgebra, Quantica

julia> h = LatticePresets.honeycomb() |> hamiltonian(hopping(1)) |> unitcell((1,-1),(30,30)) |> unitcell((1,0))
Hamiltonian{<:Lattice} : Hamiltonian on a 1D Lattice in 2D space
  Bloch harmonics  : 3 (SparseMatrixCSC, sparse)
  Harmonic size    : 120 × 120
  Orbitals         : ((:a,), (:a,))
  Element type     : scalar (ComplexF64)
  Onsites          : 0
  Hoppings         : 358
  Coordination     : 2.9833333333333334

julia> g = greens(h, SingleShot1D(), boundaries = (0,))
GreensFunction{SingleShot1DGreensSolver}: Green's function using the single-shot 1D method
  Matrix size    : 120 × 120
  Element type   : scalar (ComplexF64)
  Boundaries     : (0,)
  Reduced dims   : 60

julia> g0 = g(0.01, missing)
#391 (generic function with 1 method)

julia> ldos = @showprogress [(n,) => -imag.(diag(g0(n=>n))) for n in 1:200];
Progress: 100%|████████████████████████████████████| Time: 0:00:00

julia> vlplot(h, ldos, sitecolor = ldos -> ldos^2, sitesize = ldos -> ldos^2, maxdiameter = 10, mindiameter = 2, plotlinks = false)

Note that the cost of extending the plot to longer portions of the nanoribbon is negligible, as the 1D Greens function using the single-shot method in #150 makes this essentially free. The real bottleneck for very long nanoribbons is plotting through VegaLite

[codecov-io]

Codecov Report

Merging #152 (07356a1) into master (83ea296) will decrease coverage by 4.14%.
The diff coverage is 15.18%.

@@            Coverage Diff             @@
##           master     #152      +/-   ##
==========================================
- Coverage   66.92%   62.78%   -4.15%     
==========================================
  Files          16       16              
  Lines        3232     3450     +218     
==========================================
+ Hits         2163     2166       +3     
- Misses       1069     1284     +215     

Impacted Files	Coverage Δ
src/Quantica.jl	100.00% <ø> (ø)
src/greens.jl	0.00% <0.00%> (ø)
src/plot_vegalite.jl	0.00% <0.00%> (ø)
src/tools.jl	50.69% <50.00%> (-0.24%)	⬇️
src/hamiltonian.jl	85.73% <94.28%> (-0.18%)	⬇️
src/bandstructure.jl	86.14% <100.00%> (ø)
src/diagonalizer.jl	63.01% <100.00%> (+0.51%)	⬆️
src/iterators.jl	73.22% <100.00%> (ø)

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