Add make_supercell

Project.toml

@@ -13,7 +13,7 @@ spglib_jll = "ac4a9f1e-bdb2-5204-990c-47c8b2f70d4e"
 
 [compat]
 Graphs = "1.3"
-PeriodicGraphs = "0.8,0.9"
+PeriodicGraphs = "0.9.5"
 StaticArrays = "1.0"
 Tokenize = "0.5.8"
 julia = "1.6"

docs/Project.toml

@@ -6,4 +6,4 @@ PeriodicGraphs = "18c5b727-b240-4874-878a-f2e242435bab"
 [compat]
 Documenter = "0.27"
 Graphs = "1.3"
-PeriodicGraphs = "0.8"
+PeriodicGraphs = "0.9.5"

src/other.jl

@@ -13,4 +13,30 @@ function PeriodicGraphs.swap_axes!(pge::PeriodicGraphEmbedding{N}, t) where N
     for (i,x) in enumerate(pge.pos)
         pge.pos[i] = x[t]
     end
+    nothing
+end
+
+function PeriodicGraphs.make_supercell(cell::Cell{T}, t) where T
+    newmat = SizedMatrix{3,3,BigFloat,2,Matrix{BigFloat}}(cell.mat)
+    for i in 1:3
+        newmat[:,i] .*= t[i]
+    end
+    Cell{T}(cell.hall, newmat, cell.equivalents)
+end
+function PeriodicGraphs.make_supercell(pge::PeriodicGraphEmbedding, t)
+    g = make_supercell(pge.g, t)
+    cell = make_supercell(pge.cell, t)
+    newpos = copy(pge.pos)
+    n = length(newpos)
+    for i in 1:n
+        newpos[i] = newpos[i] ./ t
+    end
+    clock = PeriodicGraphs.MetaClock(t)
+    resize!(newpos, n*length(clock))
+    for (k, pos) in enumerate(Iterators.drop(clock, 1))
+        for i in 1:n
+            newpos[n*k+i] = newpos[i] .+ pos .// t
+        end
+    end
+    return PeriodicGraphEmbedding(g, newpos, cell)
 end

src/types.jl

@@ -488,6 +488,7 @@ end
 Base.getindex(pge::PeriodicGraphEmbedding, i::Integer) = pge.pos[i]
 Base.getindex(pge::PeriodicGraphEmbedding, u::PeriodicVertex) = pge.pos[u.v] .+ u.ofs
 Base.length(pge::PeriodicGraphEmbedding) = length(pge.pos)
+Base.copy(pge::PeriodicGraphEmbedding{D,T}) where {D,T} = PeriodicGraphEmbedding{D,T}(copy(pge.g), copy(pge.pos), pge.cell)
 
 function Base.getindex(pge::PeriodicGraphEmbedding{D,T}, vmap) where {D,T}
     PeriodicGraphEmbedding{D,T}(pge.g[vmap], pge.pos[vmap], pge.cell)

test/runtests.jl

@@ -130,3 +130,39 @@ end
     spgdataset = PeriodicGraphEmbeddings.get_spglib_dataset(mog, [mogsymms(i) for i in 1:length(mog)])
     @test spgdataset.hall_symbol == PeriodicGraphEmbeddings.get_spglib_dataset(mog).hall_symbol
 end
+
+@testset "Complex modifications" begin
+    itn = PeriodicGraphEmbedding(
+        PeriodicGraph3D("3 1 28 0 0 0 1 29 0 0 0 1 77 0 0 1 1 157 -1 0 0 2 29 0 0 0 2 30 0 0 0 2 31 0 0 0 2 33 0 0 0 3 31 0 0 0 3 32 0 0 0 3 40 0 0 1 3 127 -1 0 0 4 33 0 0 0 4 34 0 0 0 4 35 0 0 0 4 36 0 0 0 5 36 0 0 0 5 37 0 0 0 5 38 0 0 0 5 79 0 1 0 6 38 0 0 0 6 39 0 0 0 6 43 0 0 0 6 47 0 0 0 7 39 0 0 0 7 40 0 0 0 7 41 0 0 0 7 42 0 0 0 8 43 0 -1 0 8 44 0 0 0 8 45 0 0 0 8 46 0 0 0 9 47 0 0 0 9 48 0 0 0 9 49 0 0 0 9 50 0 0 0 10 35 0 0 0 10 50 0 0 0 10 51 0 0 0 10 52 0 0 0 11 52 0 0 0 11 53 0 0 0 11 54 0 0 0 11 138 0 0 1 12 54 0 0 0 12 55 0 0 0 12 56 0 0 0 12 57 0 0 0 13 49 0 0 0 13 57 0 0 0 13 58 0 0 0 13 62 0 0 0 14 58 0 0 0 14 59 0 0 0 14 60 0 0 0 14 67 0 1 0 15 51 0 0 0 15 60 0 0 0 15 61 0 0 0 15 150 0 0 1 16 62 0 0 0 16 63 0 0 0 16 64 0 1 0 16 146 0 0 0 17 65 0 0 0 17 66 0 0 0 17 67 0 0 0 17 68 0 0 0 18 55 0 0 0 18 68 0 0 0 18 69 0 0 0 18 70 0 0 0 19 53 0 0 0 19 70 0 0 0 19 71 0 0 0 19 141 0 0 1 20 61 0 -1 0 20 71 0 0 0 20 72 0 0 0 20 73 0 0 0 21 48 0 -1 0 21 66 0 0 0 21 73 0 0 0 21 74 0 0 0 22 46 0 0 0 22 74 0 0 0 22 75 0 0 0 22 78 0 0 0 23 42 0 0 0 23 75 0 0 0 23 76 0 0 0 23 77 0 0 0 24 78 0 0 0 24 79 0 0 0 24 80 0 0 0 24 112 -1 0 0 25 34 0 -1 0 25 72 0 0 0 25 80 0 0 0 25 81 0 0 0 26 32 0 -1 0 26 81 0 0 0 26 82 0 0 0 26 119 -1 0 0 27 28 0 0 0 27 44 0 0 1 27 82 0 0 0 27 123 -1 0 0 30 106 -1 0 0 37 108 -1 0 0 41 109 -1 0 0 45 85 -1 0 0 56 93 0 0 1 59 101 0 0 1 64 98 0 0 0 65 98 0 0 0 69 97 0 0 1 76 83 -1 0 0 83 110 0 0 0 83 111 0 0 0 83 158 0 0 -1 84 111 0 0 0 84 112 0 0 0 84 113 0 0 0 84 115 0 0 0 85 113 0 0 0 85 114 0 0 0 85 122 0 0 -1 86 115 0 0 0 86 116 0 0 0 86 117 0 0 0 86 118 0 0 0 87 118 0 0 0 87 119 0 0 0 87 120 0 0 0 87 160 0 -1 0 88 120 0 0 0 88 121 0 0 0 88 125 0 0 0 88 129 0 0 0 89 121 0 0 0 89 122 0 0 0 89 123 0 0 0 89 124 0 0 0 90 125 0 1 0 90 126 0 0 0 90 127 0 0 0 90 128 0 0 0 91 129 0 0 0 91 130 0 0 0 91 131 0 0 0 91 132 0 0 0 92 117 0 0 0 92 132 0 0 0 92 133 0 0 0 92 134 0 0 0 93 134 0 0 0 93 135 0 0 0 93 136 0 0 0 94 136 0 0 0 94 137 0 0 0 94 138 0 0 0 94 139 0 0 0 95 131 0 0 0 95 139 0 0 0 95 140 0 0 0 95 144 0 0 0 96 140 0 0 0 96 141 0 0 0 96 142 0 0 0 96 148 0 -1 0 97 133 0 0 0 97 142 0 0 0 97 143 0 0 0 98 144 0 0 0 98 145 0 0 0 99 146 0 0 0 99 147 0 0 0 99 148 0 0 0 99 149 0 0 0 100 137 0 0 0 100 149 0 0 0 100 150 0 0 0 100 151 0 0 0 101 135 0 0 0 101 151 0 0 0 101 152 0 0 0 102 143 0 1 0 102 152 0 0 0 102 153 0 0 0 102 154 0 0 0 103 130 0 1 0 103 147 0 0 0 103 154 0 0 0 103 155 0 0 0 104 128 0 0 0 104 155 0 0 0 104 156 0 0 0 104 159 0 0 0 105 124 0 0 0 105 156 0 0 0 105 157 0 0 0 105 158 0 0 0 106 159 0 0 0 106 160 0 0 0 106 161 0 0 0 107 116 0 1 0 107 153 0 0 0 107 161 0 0 0 107 162 0 0 0 108 114 0 1 0 108 162 0 0 0 108 163 0 0 0 109 110 0 0 0 109 126 0 0 -1 109 163 0 0 0"),
+        SVector{3, Float64}[[0.05179, 0.48234, 0.91511], [0.07258, 0.70899, 0.79527], [0.05733, 0.85943, 0.91674], [0.1567, 0.81073, 0.70182], [0.0769, 0.8981, 0.42328], [0.16828, 0.85774, 0.34649], [0.10153, 0.72914, 0.17864], [0.09116, 0.1094, 0.1678], [0.31108, 0.85323, 0.56472], [0.30251, 0.71347, 0.78004], [0.39421, 0.47891, 0.91981], [0.49287, 0.50757, 0.83426], [0.45775, 0.75419, 0.66662], [0.49044, 0.89125, 0.8331], [0.39214, 0.86637, 0.90875], [0.47586, 0.88681, 0.47318], [0.45639, 0.13865, 0.65411], [0.48678, 0.26845, 0.82588], [0.38987, 0.24291, 0.90373], [0.29803, 0.10165, 0.77347], [0.31039, 0.10906, 0.56289], [0.16553, 0.2431, 0.33869], [0.09973, 0.48917, 0.16751], [0.07315, 0.14459, 0.41455], [0.15287, 0.05735, 0.69252], [0.06908, 0.09844, 0.7854], [0.04591, 0.24206, 0.90486], [0.07263, 0.35707, 0.92175], [0.0725, 0.57489, 0.83972], [0.00058, 0.77428, 0.6721], [0.08608, 0.75961, 0.89576], [0.08104, 0.97465, 0.87782], [0.13104, 0.72591, 0.77318], [0.17104, 0.92004, 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+        Cell(1, (24.2005, 12.5399, 14.2502), (72.599, 123.128, 90.0))
+    )
+    n = length(itn)
+    itncopy = copy(itn)
+    @test itncopy == itn !== itncopy
+
+    itnoffset = copy(itncopy)
+    offset_representatives!(itnoffset, [(-i,2,i+1) for i in 1:n])
+    @test itn == itncopy != itnoffset
+    for i in 1:n
+        @test Float32.(itn[i]) == Float32.(itnoffset[PeriodicVertex(i, (-i,2,i+1))])
+    end
+
+    itnrotated = copy(itncopy)
+    swap_axes!(itnrotated, [2,3,1])
+    @test itn == itncopy != itnrotated
+    for i in 1:n
+        @test itn[i][[2,3,1]] == itnrotated[i]
+    end
+
+    itn312 = make_supercell(itn, (3, 1, 2))
+    @test itn312 == make_supercell(itn, SVector{3,Int}(3, 1, 2)) == make_supercell(itn, [3, 1, 2])
+    mat = itn.cell.mat
+    mat312 = itn312.cell.mat
+    for p in PeriodicGraphs.MetaClock([3, 1, 2])
+        factor = n*(p[1] + 3*p[2] + 3*p[3])
+        for i in 1:n
+            @test Float32.(mat*itn[PeriodicVertex3D(i, p)]) == Float32.(mat312*itn312[factor+i])
+        end
+    end
+end