Merge branch 'master' into bandpaths-data

Author: thchr

.github/workflows/ci.yml

@@ -21,29 +21,21 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v4
+      - uses: actions/cache@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v1
       - run: | # force use of the local version of Bravais (instead of just the latest registered version)
           julia --color=yes --project -e '
             using Pkg
             Pkg.develop(PackageSpec(path=joinpath(pwd(), "Bravais")))'
         shell: bash # avoid escaping issues w/ pwsh on Windows (cf. https://github.com/julia-actions/setup-julia#matrix-testing)
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
         continue-on-error: ${{ matrix.version == 'nightly' }}
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v3
         with:
-          file: lcov.info
+          file: lcov.info

build/setup_2d_band_representations.jl

@@ -5,7 +5,7 @@ using Crystalline: irdim, constant, free, AbstractIrrep, iscorep,
 import Crystalline: mulliken, realify, group
 using StaticArrays
 
-# The implementation here follows Elcoro et al., Phys. Rev. B 97, 035139 (2018)
+# The implementation here follows Cano et al., Phys. Rev. B 97, 035139 (2018)
 # (https://doi.org/10.1103/PhysRevB.97.035139), specifically, Sections II.C-D
 
 # ---------------------------------------------------------------------------------------- #

build/setup_2d_littlegroup_irreps.jl

@@ -5,8 +5,8 @@ using Crystalline
 # every group. The notation follows Bilbao's LKVEC tool [^1] entirely. Note that this
 # implies some occasionally odd-looking choices, e.g. (see (*) marks below):
 #   - *Plane groups 3 & 4*: the X and Y labels are defined counter-intuitively, such that
-#           X = (0,1/2) and Y = (1/2,0). This also differs from the definitions in other
-#           the other primitive rectangular (op) Bravais lattices (i.e. 6, 7, & 8), which
+#           X = (0,1/2) and Y = (1/2,0). This also differs from the definitions in the
+#           other primitive rectangular (op) Bravais lattices (i.e. 6, 7, & 8), which
 #           instead have X = (1/2,0) etc. The difference also exists for k-line labels.
 #   - *Plane group 5 vs. 9*: although both are centred rectangular (oc) Bravais lattices,
 #           their k-vector labels do not agree, but differ by coordinate permutations.

ext/CrystallineGraphMakieExt.jl

@@ -235,7 +235,7 @@ end
 
 function Makie.plot(gr::GroupRelationGraph;
                     axis = NamedTuple(), figure = NamedTuple(), kws...)
-    f = Makie.Figure(resolution=(800,900); figure...)
+    f = Makie.Figure(size=(800,900); figure...)
     f[1,1] = ax = Makie.Axis(f; axis...)
     p = Makie.plot!(ax, gr; kws...)
     return Makie.FigureAxisPlot(f, ax, p)

src/grouprelations/show.jl

@@ -5,6 +5,7 @@ function Base.summary(io::IO, rels::GroupRelations{D,AG}) where {D,AG}
     print(io, "GroupRelations{", AG, "} ⋕", rels.num, " (", iuc(rels.num, D), 
               ") with ", length(rels), " elements")
 end
+
 function Base.summary(io::IO, rel::GroupRelation{D,AG}) where {D,AG}
     print(io, "GroupRelation{", AG, "} ⋕", rel.num)
     printstyled(io, is_tgleiche(rel.kind) ? "ᵀ" : "ᴷ"; 
@@ -18,15 +19,24 @@ function Base.show(io::IO, ::MIME"text/plain", rels::GroupRelations{D,AG}) where
     summary(io, rels)
     print(io, ":")
     for rel in values(rels)
-        print(io, '\n')
+        print(io, "\n ")
         _print_child(io, rel.num, rel.kind, rel.index)
     end
 end
 
-function _print_child(io::IO, num::Int, kind::GleicheKind, index::Int)
-    print(io, " ⋕", num)
-    printstyled(io, is_tgleiche(kind) ? "ᵀ" : "ᴷ", color = is_tgleiche(kind) ? :green : :red)
-    print(io, " (index ", index, ")")
+function _print_child(
+            io::IO, 
+            num::Int,
+            kind::Union{Nothing, GleicheKind},
+            index::Union{Nothing, Int})
+    print(io, "⋕", num)
+    if !isnothing(kind)
+        printstyled(io, is_tgleiche(kind) ? "ᵀ" : "ᴷ";
+                        color = is_tgleiche(kind) ? :green : :red)
+    end
+    if !isnothing(index)
+        printstyled(io, " (index ", index, ")"; color=:light_black)
+    end
 end
 
 function Base.show(io::IO, rels::GroupRelations{D,AG}) where {AG,D}
@@ -40,6 +50,7 @@ function Base.show(io::IO, rels::GroupRelations{D,AG}) where {AG,D}
     end
     print(io, "]")
 end
+
 function Base.show(io::IO, ::MIME"text/plain", g::GroupRelation)
     summary(io, g)
     print(io, ":")
@@ -48,6 +59,7 @@ function Base.show(io::IO, ::MIME"text/plain", g::GroupRelation)
         print(io, ct)
     end
 end
+
 function Base.show(io::IO, t::ConjugacyTransform{D}) where D
     print(io, "P = ")
     if isnothing(t.P) && isnothing(t.p)
@@ -64,4 +76,69 @@ function Base.show(io::IO, t::ConjugacyTransform{D}) where D
                       replace(string(rationalize.(float(p))), r"//1([,|\]])"=>s"\1", "//"=>"/", "Rational{Int64}"=>""))
         end
     end
+end
+
+function Base.summary(io::IO, gr::GroupRelationGraph{D, AG}) where {D,AG}
+    print(io, "GroupRelationGraph",
+              " (", gr.direction == SUPERGROUP ? "super" : "sub", "groups)",
+              " of ", AG, " ⋕", first(gr.nums), 
+              " with ", length(gr.nums), " vertices")
+end
+function Base.show(io::IO, gr::GroupRelationGraph)
+    summary(io, gr)
+    print(io, ":")
+    num = first(gr.nums) # find "base" group number
+    _print_graph_leaves(io, gr, num, Bool[], nothing, nothing)
+end
+function _print_graph_leaves(
+            io::IO, 
+            gr::GroupRelationGraph, 
+            num::Int, 
+            is_last::Vector{Bool}, 
+            kind::Union{Nothing, GleicheKind}, 
+            index::Union{Nothing, Int}
+            )
+
+    # indicate "structure"-relationship of graph "leaves"/children via box-characters
+    indent = length(is_last)
+    print(io, "\n ")
+    if indent ≥ 2
+        for l in 1:indent-1
+            if !is_last[l]
+                printstyled(io, "│"; color=:light_black)
+                print(io, "  ")
+            else
+                print(io, "   ")
+            end
+        end
+    end
+    if indent > 0
+        printstyled(io, last(is_last) ? "└" : "├", "─►"; color=:light_black)
+    end
+
+    # print info about child
+    _print_child(io, num, kind, index)
+
+    # now move on to children of current child; print info about them, recursively
+    if !isnothing(kind) && kind == KLASSENGLEICHE
+        # avoid printing recursively for klassengleiche as this implies infinite looping
+        # NB: in principle, this means we don't show the entire structure of 
+        #     `gr.infos`; but it is also really not that clear how to do this
+        #     properly for klassengleiche relations which are not a DAG but often 
+        #     cyclic
+
+    # only one child and child is trivial group
+    elseif length(gr.infos[num].children) == 1 && gr.infos[num].children[1].num == 1
+        child = gr.infos[num].children[1]
+        printstyled(io, "  ╌╌►"; color=:light_black)
+        _print_child(io, child.num, child.kind, child.index)
+    
+    # multiple children/nontrivial children
+    else
+        N_children = length(gr.infos[num].children)
+        for (i,child) in enumerate(gr.infos[num].children)
+            child_is_last = vcat(is_last, i==N_children)
+            _print_graph_leaves(io, gr, child.num, child_is_last, child.kind, child.index)
+        end
+    end
 end

src/grouprelations/types.jl

@@ -44,7 +44,7 @@ struct GroupRelationGraph{D,AG} <: Graphs.AbstractGraph{Int}
     direction :: RelationKind # whether this is a sub- or supergroup relation
 end
 dim(::GroupRelationGraph{D}) where D = D
-
+Base.getindex(gr::GroupRelationGraph, i::Integer) = getindex(gr.infos, i)
 # ---------------------------------------------------------------------------------------- #
 # Graphs.jl `AbstractGraph` interface for `GroupRelationGraph`
 

src/notation.jl

@@ -478,8 +478,8 @@ Return the Mulliken label of a point group irrep `pgir`.
 
 ## Notes
 This functionality is a simple mapping between the tabulated CDML point group irrep labels
-and associated Mulliken labels, using the listings from the Bilbao Crystallographic
-Database [^1].
+and associated Mulliken labels [^1], using the listings from the Bilbao Crystallographic
+Database [^2].
 
 Ignoring subscript, the rough rules associated with assignment of Mulliken labels are:
 
@@ -498,7 +498,9 @@ Ignoring subscript, the rough rules associated with assignment of Mulliken label
    describe here.
 
 ## References
-[^1]: Bilbao Crystallographic Database's
+[^1]: Mulliken, Report on Notation for the Spectra of Polyatomic Molecules, 
+      [J. Chem. Phys. *23*, 1997 (1955)](https://doi.org/10.1063/1.1740655).
+[^2]: Bilbao Crystallographic Database's
       [Representations PG program](https://www.cryst.ehu.es/cgi-bin/cryst/programs/representations_point.pl?tipogrupo=spg).
 """
 function mulliken(pgir::PGIrrep{D}) where D

src/pointgroup.jl

@@ -106,14 +106,16 @@ end
 Return the (crystallographic) point group irreps of the IUC label `iuclab` of dimension `D`
 as a `Vector{PGIrrep{D}}`.
 
+See `Crystalline.PG_IUC2NUM[D]` for possible IUC labels in dimension `D`.
+
 ## Notation
 
 The irrep labelling follows the conventions of CDML [^1] [which occasionally differ from
 those in e.g. Bradley and Cracknell, *The Mathematical Theory of Symmetry in Solids* 
 (1972)].
 
 To use Mulliken ("spectroscopist") irrep labels instead, set the keyword argument
-`mulliken = true` (default, `false). See also [`mulliken`](@ref).
+`mulliken = true` (default, `false`). See also [`mulliken`](@ref).
 
 ## Data sources
 

src/utils.jl

@@ -254,7 +254,7 @@ end
 # === misc functionality ===
 
 """
-    isapproxin(x, itr) --> Bool
+    isapproxin(x, itr, optargs...; kwargs...) --> Bool
 
 Determine whether `x` ∈ `itr` with approximate equality.
 """