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add irreducible brillouin visualization for 3d #43

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Nov 3, 2022
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add irreducible brillouin visualization for 3d #43

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41 changes: 36 additions & 5 deletions toolbox/plotlyjs_wignerseitz.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,7 @@ using .PlotlyJS
import .PlotlyJS: plot
using LinearAlgebra: norm, dot
using StaticArrays

using .WignerSeitz: face_normal
using .WignerSeitz: face_normal, merge_coplanar!
# ---------------------------------------------------------------------------------------- #
# CONSTANTS

Expand Down Expand Up @@ -118,8 +117,8 @@ function plot(c::Cell{3}, layout::Layout=Layout();
ts = vcat(tbz, tgs, tgtips, taxs, taxtips)
return PlotlyJS.plot(ts, layout; config=config)
end

function plot(clist::Array{Cell{3}}, idx_center::Int, layout::Layout=Layout();
function plot(clist::Array{Cell{3}}, idx_center::Int, layout::Layout=Layout(); ibz=nothing,
config::PlotConfig=PlotConfig(responsive=true, displaylogo=false))

layout = merge(DEFAULT_PLOTLY_LAYOUT_3D, layout)
Expand All @@ -134,7 +133,38 @@ function plot(clist::Array{Cell{3}}, idx_center::Int, layout::Layout=Layout();
taxs = Vector{GenericTrace{Dict{Symbol,Any}}}(undef, 6)
taxtips = Vector{GenericTrace{Dict{Symbol,Any}}}(undef, 3)


if !isnothing(ibz)
facecolor = repeat([
"rgb(50, 200, 200)",
"rgb(100, 200, 255)",
"rgb(150, 200, 115)",
"rgb(200, 200, 50)",
"rgb(230, 200, 10)",
"rgb(255, 140, 0)"
], inner=[2])
setting(ibz) !== CARTESIAN && (ibz = cartesianize(ibz))
faces = PlotlyJS.mesh3d(x=[ibz.verts[i][1] for i in 1:length(ibz.verts)],
y=[ibz.verts[i][2] for i in 1:length(ibz.verts)],
z=[ibz.verts[i][3] for i in 1:length(ibz.verts)],
i=[ibz.faces[i][1]-1 for i in 1:length(ibz.faces)],
j=[ibz.faces[i][2]-1 for i in 1:length(ibz.faces)],
k=[ibz.faces[i][3]-1 for i in 1:length(ibz.faces)],
facecolor = facecolor, opacity=0.7
)
merge_coplanar!(ibz) # Coplanar triangles have to be merged after calling mesh3d.
# BZ
tbz = Vector{GenericTrace{Dict{Symbol,Any}}}(undef, length(ibz)+1)
for (i, poly) in enumerate(ibz)
tbz[i] = PlotlyJS.scatter3d(
x=push!(getindex.(poly, 1), poly[1][1]),
y=push!(getindex.(poly, 2), poly[1][2]),
z=push!(getindex.(poly, 3), poly[1][3]);
mode="lines", hovertext="Cell", hoverinfo="text+x+y+z",
line=attr(color=BZ_COL[], width=3))
end
tbz[length(ibz)+1] = faces
push!(tbz_list, tbz)
end
for (ci, c) in enumerate(clist)
if (!isnothing(c))
setting(c) !== CARTESIAN && (c = cartesianize(c))
Expand Down Expand Up @@ -207,6 +237,7 @@ function plot(clist::Array{Cell{3}}, idx_center::Int, layout::Layout=Layout();
end
end
end

# combine traces and plot
ts = tbz_list[1]
for i in 2:length(tbz_list)
Expand Down
54 changes: 46 additions & 8 deletions toolbox/test_extend.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,9 @@ using BrillouinZoneMeshes
using PyCall
const PySpatial = PyNULL()
using BrillouinZoneMeshes.LinearAlgebra
using SymmetryReduceBZ.Symmetry:calc_ibz
import SymmetryReduceBZ.Utilities: get_uniquefacets
import QHull
include("default_colors.jl")
include("plotlyjs_wignerseitz.jl")
function wignerseitz_ext(basis::AVec{<:SVector{D,<:Real}};
Expand Down Expand Up @@ -41,6 +44,7 @@ function wignerseitz_ext(basis::AVec{<:SVector{D,<:Real}};
vor = PySpatial.Voronoi(lattice) # voronoi tesselation of lattice
clist = Cell{D}[]
idx_center_final = 0

# grab all the vertices of the central voronoi region enclosing origo
# for idx_cntr in 1:length(vor.point_region)
for idx_cntr in 1:length(vor.point_region)
Expand Down Expand Up @@ -69,6 +73,19 @@ function wignerseitz_ext(basis::AVec{<:SVector{D,<:Real}};
return clist, idx_center_final
end

function convert_to_cell(hull::QHull.Chull{Float64}, basis::AVec{<:SVector{D,<:Real}}) where D
# The QHull julia package is used by SymmetryReduceBZ, whereas Brillouin package use Qhull from
# SciPy instead. Therefore we have to reload this function for julia QHull object.
vs′ = hull.points # vertices
simp = hvcat(size(hull.simplices,1),hull.simplices...)'
fs′ = simp # faces

vs = SVector{D, Float64}.(eachrow(vs′))
fs = Vector{Int}.(eachrow(fs′))
return Cell(vs, fs, SVector{D, SVector{D, Float64}}(basis), Ref(CARTESIAN))
end


function wignerseitz_ext(basis::AVec{<:AVec{<:Real}}; kwargs...)
D = length(first(basis))
all(V -> length(V) == D, @view basis[2:end]) || error(DomainError(basis, "provided `basis` must have identical dimensions"))
Expand All @@ -77,6 +94,7 @@ function wignerseitz_ext(basis::AVec{<:AVec{<:Real}}; kwargs...)
end



# Wigner-Seitz cells visualization
# 2D
#Rs = [[1.0, 0.0], [-0.5, √3/2]]
Expand All @@ -89,22 +107,42 @@ end
# latvec = [1 0; 0 1]'
# 3D

lattice = [[0 1 1.0]; [1 0 1.0]; [1 1 0.0]]
atoms = [1, 1]
positions = [ones(3) / 8, -ones(3) / 8]
br = BZMeshes.Brillouin(lattice=lattice, atoms=atoms, positions=positions)
lattice = [[0 0.5 0.5]; [0.5 0 0.5]; [0.5 0.5 0.0]]
#atoms = [1,1]
#positions = [ones(3) / 8, -ones(3) / 8]

#lattice = [[1.0 0.0 0.0]; [0.0 1.0 0.0]; [0.0 0.0 1.0]]
atoms = [1]
positions = [zeros(3)]

atom_pos = hvcat(size(positions,1),positions...)
ibzformat = "convex hull"
coordinates = "Cartesian"
makeprim = true
convention = "ordinary"

br = BZMeshes.Brillouin(lattice=lattice, atoms=atoms, positions=positions)
#br = BZMeshes.Brillouin(lattice=lattice)
msize = (4, 4, 4)

bzmesh = UniformBZMesh(br=br, size=msize)

meshmap = MeshMap(bzmesh)

latvec = mapslices(x -> [x], lattice_vector(bzmesh), dims=1)[:]
clist, idx_center = wignerseitz_ext(latvec, cut=1)
recip_lattice=lattice_vector(bzmesh)
#latvec = mapslices(x -> [x],recip_lattice , dims=1)[:]
latvec = mapslices(x -> [x], recip_lattice , dims=1)[:]

#generate irreducible brillouin zone
ibz = calc_ibz(lattice./2/π,atoms, atom_pos, coordinates,ibzformat,
makeprim,convention)
#The 1/2π here is due to the convention difference between packages. SymmetryReduceBZ has a \dot a_recip = 1 instead of 2π

P = plot(clist, idx_center)
c = convert_to_cell(ibz, SVector{length(latvec[1]),Float64}.(latvec))
c = WignerSeitz.reorient_normals!(c)
latticize!(c) # Do not merge coplanar triangles for reduced mesh. This must be done within plot.

clist, idx_center = wignerseitz_ext(latvec, cut=1)
P = plot(clist, idx_center, ibz=c)

fullmesh = [bzmesh[i] for i in 1:length(bzmesh)]
reducedmesh = [bzmesh[i] for i in meshmap.irreducible_indices]
Expand Down