Merge pull request #234 from pablosanjose/CellIndices

Refactor of LatticeSlice and Contacts

Project.toml

@@ -7,10 +7,10 @@ version = "1.0.1"
 ArnoldiMethod = "ec485272-7323-5ecc-a04f-4719b315124d"
 Arpack = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
+Dictionaries = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4"
 ExprTools = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
 FrankenTuples = "7e584817-dab4-53a9-9a51-4037a36b0ad0"
 FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
-GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
 KrylovKit = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -27,6 +27,7 @@ SuiteSparse = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 
 [weakdeps]
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 
 [extensions]
 QuanticaMakieExt = "Makie"
@@ -42,12 +43,13 @@ GeometryBasics = "0.4"
 IntervalTrees = "1"
 KrylovKit = "0.6"
 LinearMaps = "3"
-Makie = "0.19.3, 0.20, 1.0"
+Makie = "0.20, 1.0"
 NearestNeighbors = "0.4"
 ProgressMeter = "1.2"
 QuadGK = "2"
 SpecialFunctions = "2"
 StaticArrays = "0.12.3, 0.13, 1.0"
+Dictionaries = "0.3.26"
 julia = "^1.9"
 
 [extras]

docs/src/tutorial/lattices.md

@@ -113,7 +113,7 @@ julia> qplot(lat, hide = nothing)
     GLMakie.jl is optimized for interactive GPU-accelerated, rasterized plots. If you need to export to PDF for publications or display plots inside a Jupyter notebook, use CairoMakie.jl instead, which in general renders non-interactive, but vector-based plots.
 
 !!! tip "User-defined defaults for `qplot`"
-    The command `qplotdefaults(; axis, figure)` can be used to define the default value of `figure` and `axis` keyword arguments of `qplot`. Example: to fix the resolution of all subsequent plots, do `qplotdefaults(; figure = (resolution = (1000, 1000),))`.
+    The command `qplotdefaults(; axis, figure)` can be used to define the default value of `figure` and `axis` keyword arguments of `qplot`. Example: to fix the size of all subsequent plots, do `qplotdefaults(; figure = (size = (1000, 1000),))`.
 
 ## [SiteSelectors](@id siteselectors)
 

ext/QuanticaMakieExt/defaults.jl

@@ -63,7 +63,7 @@ checkplotdim(::PlotArgumentType{E}) where {E} =
 
 ## plotlattice defaults
 
-const plotlat_default_figure = (; resolution = (1200, 1200), fontsize = 40)
+const plotlat_default_figure = (; size = (1200, 1200), fontsize = 40)
 
 const plotlat_default_axis3D = (;
     xlabel = "x", ylabel = "y", zlabel = "z",
@@ -86,7 +86,7 @@ const plotlat_default_3D =
 
 ## plotbands defaults
 
-const plotbands_default_figure = (; resolution = (1200, 1200), fontsize = 40)
+const plotbands_default_figure = (; size = (1200, 1200), fontsize = 40)
 
 const plotbands_default_axis3D = (;
     xlabel = "ϕ₁", ylabel = "ϕ₂", zlabel = "ε",

ext/QuanticaMakieExt/docstrings.jl

@@ -21,7 +21,7 @@ cycling over them if necessary.
 
 ## Keywords
 
-- `figure`: keywords to pass onto the plot `Figure` (e.g. `resolution` or `fontsize`, see `Makie.Figure`)
+- `figure`: keywords to pass onto the plot `Figure` (e.g. `size` or `fontsize`, see `Makie.Figure`)
 - `axis`: keywords to pass on to the plot axis (see `Makie.LScene`, `Makie.Axis3` or `Makie.Axis` for options)
 - `fancyaxis::Bool`: for 3D plots, whether to use `Makie.LScene` (supports zoom+pan) instead of `Makie.Axis3`
 - `inspector::Bool`: whether to enable interactive tooltips of plot elements
@@ -158,11 +158,11 @@ Equivalent to `qplotdefaults(; defaults...)`
 
 # Examples
 ```jldoctest
-julia> qplotdefaults(figure = (resolution = (1000, 1000),))
-(user_default_figure = (resolution = (1000, 1000),), user_default_axis2D = NamedTuple(), user_default_axis3D = NamedTuple(), user_default_lscene = NamedTuple(), user_default_inspector = NamedTuple())
+julia> qplotdefaults(figure = (size = (1000, 1000),))
+(user_default_figure = (size = (1000, 1000),), user_default_axis2D = NamedTuple(), user_default_axis3D = NamedTuple(), user_default_lscene = NamedTuple(), user_default_inspector = NamedTuple())
 
 julia> qplotdefaults(axis2D = (xlabel = "X",), inspector = (fontsize = 30,))
-(user_default_figure = (resolution = (1000, 1000),), user_default_axis2D = (xlabel = "X",), user_default_axis3D = NamedTuple(), user_default_lscene = NamedTuple(), user_default_inspector = (fontsize = 30,))
+(user_default_figure = (size = (1000, 1000),), user_default_axis2D = (xlabel = "X",), user_default_axis3D = NamedTuple(), user_default_lscene = NamedTuple(), user_default_inspector = (fontsize = 30,))
 ```
 """
 qplotdefaults

ext/QuanticaMakieExt/plotbands.jl

@@ -185,7 +185,7 @@ function plotmeshes!(plot, mp::MeshPrimitives{<:Any,3})
         if !ishidden((:wireframe, :simplices), plot)
             color´ = darken.(mp.colors, plot[:nodedarken][])
             poly!(plot, mp.verts, simps; color = mp.colors, inspectable = false, transparency,
-                 strokewidth = plot[:size][], shading = true)
+                 strokewidth = plot[:size][])
         else
             mesh!(plot, mp.verts, simps; color = mp.colors, inspectable = false, transparency)
         end

ext/QuanticaMakieExt/plotlattice.jl

@@ -550,7 +550,7 @@ function plotbravais!(plot::PlotLattice, lat::Lattice{<:Any,E,L}, latslice) wher
         mrect0 = GeometryBasics.mesh(rect, pointtype=Point{L,Float32}, facetype=QuadFace{Int})
         vertices0 = mrect0.position
         mat = Quantica.bravais_matrix(bravais)
-        for sc in Quantica.subcells(latslice)
+        for sc in Quantica.cellsdict(latslice)
             cell = Quantica.cell(sc)
             mrect = GeometryBasics.mesh(rect, pointtype=Point{E,Float32}, facetype=QuadFace{Int})
             vertices = mrect.position

src/Quantica.jl

@@ -9,6 +9,7 @@ using NearestNeighbors
 using SparseArrays
 using SparseArrays: getcolptr, AbstractSparseMatrix, AbstractSparseMatrixCSC
 using LinearAlgebra
+using Dictionaries
 using ProgressMeter
 using Random
 using SuiteSparse

src/apply.jl

@@ -236,6 +236,9 @@ function apply(solver::AbstractEigenSolver, h::AbstractHamiltonian, ::Type{S}, m
         apply_transform!(eigen, transform)
         return eigen
     end
+    # for some reason, unless this is called, h´ may be GC'ed despite the asolver closure in
+    # some systems, leading to segfaults. TODO: clarify why this is needed
+    sfunc(zero(S))
     asolver = AppliedEigenSolver(FunctionWrapper{EigenComplex{T},Tuple{S}}(sfunc))
     return asolver
 end

src/bands.jl

@@ -255,7 +255,7 @@ end
 
 function subbands_diagonalize!(data)
     baseverts = vertices(data.basemesh)
-    meter = Progress(length(baseverts), "Step 1 - Diagonalizing: ")
+    meter = Progress(length(baseverts); desc = "Step 1 - Diagonalizing: ")
     push!(data.coloffsets, 0) # first element
     if length(data.solvers) > 1
         Threads.@threads :static for i in eachindex(baseverts)
@@ -327,7 +327,7 @@ end
 #region
 
 function subbands_knit!(data)
-    meter = Progress(length(data.eigens), "Step 2 - Knitting: ")
+    meter = Progress(length(data.eigens); desc = "Step 2 - Knitting: ")
     for isrcbase in eachindex(data.eigens)
         for idstbase in neighbors_forward(data.basemesh, isrcbase)
             knit_seam!(data, isrcbase, idstbase)
@@ -401,8 +401,8 @@ function subbands_patch!(data)
     queue_frustrated!(data)
     data.warn && isempty(data.defects) &&
         @warn "Trying to patch $(length(data.frustrated)) band dislocations without a list `defects` of defect positions."
-    meter = data.patches < Inf ? Progress(data.patches, "Step 3 - Patching: ") :
-                                 ProgressUnknown("Step 3 - Patching: ")
+    meter = data.patches < Inf ? Progress(data.patches; desc = "Step 3 - Patching: ") :
+                                 ProgressUnknown(; desc = "Step 3 - Patching: ")
     newcols = 0
     done = false
     while !isempty(data.frustrated) && !done
@@ -567,7 +567,7 @@ function subbands_split!(data)
         # vsinds are the subband index of each vertex index
         # svinds is lists of band vertex indices that belong to the same subband
         vsinds, svinds = subsets(data.bandneighs)
-        meter = Progress(length(svinds), "Step 4 - Splitting: ")
+        meter = Progress(length(svinds); desc = "Step 4 - Splitting: ")
         new2old = sortperm(vsinds)
         old2new = invperm(new2old)
         offset = 0
@@ -607,7 +607,7 @@ end
 
 function subband_projectors!(data)
     nsimps = sum(s -> length(simplices(s)), data.subbands)
-    meter = Progress(nsimps, "Step 5 - Projectors: ")
+    meter = Progress(nsimps; desc = "Step 5 - Projectors: ")
     if data.projectors
         for s in data.subbands
             subband_projectors!(s, data.hf, meter, data.showprogress)

src/docstrings.jl

@@ -1398,11 +1398,11 @@ julia> gdisk = HP.graphene(a0 = 1, dim = 3) |> supercell(region = RP.circle(10))
 attach
 
 """
-    cellsites(cell_indices, site_indices)
+    cellsites(cell_index, site_indices)
 
-Simple selector of sites with given `site_indices` in a given cell at `cell_indices`. Here,
+Simple selector of sites with given `site_indices` in a given cell at `cell_index`. Here,
 `site_indices` can be an index, a collection of integers or `:` (for all sites), and
-`cell_indices` should be a collection of `L` integers, where `L` is the lattice dimension.
+`cell_index` should be a collection of `L` integers, where `L` is the lattice dimension.
 
 # See also
     `siteselector`