/
bzmesh.jl
115 lines (94 loc) · 4.34 KB
/
bzmesh.jl
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using DFTK
using LinearAlgebra
using PyCall
using Test
using Unitful
include("testcases.jl")
@testset "bzmesh_uniform agrees with spglib" begin
function test_against_spglib(kgrid_size; kshift=[0, 0, 0])
kgrid_size = Vec3(kgrid_size)
is_shift = ifelse.(kshift .== 0, 0, 1)
n_kpts, _, grid =
DFTK.spglib_get_stabilized_reciprocal_mesh(kgrid_size, [Matrix{Int64}(I, 3, 3)],
is_shift=is_shift)
kcoords_spglib = [(kshift .+ grid[ik]) .// kgrid_size
for ik in 1:n_kpts]
kcoords_spglib = DFTK.normalize_kpoint_coordinate.(kcoords_spglib)
sort!(kcoords_spglib)
kcoords, _ = bzmesh_uniform(kgrid_size, kshift=kshift)
sort!(kcoords)
@test kcoords == kcoords_spglib
end
test_against_spglib([ 2, 3, 2])
test_against_spglib([ 3, 3, 3])
test_against_spglib([ 3, 3, 3], kshift=[1//2, 0, 0])
test_against_spglib([ 2, 3, 4])
test_against_spglib([ 9, 11, 13])
end
@testset "bzmesh_ir_wedge is correct reduction" begin
function test_reduction(system, kgrid_size, kirredsize;
supercell=[1, 1, 1], kshift=[0, 0, 0])
lattice = system.lattice
atoms = [ElementCoulomb(system.atnum) => system.positions]
if supercell != [1, 1, 1] # Make a supercell
pystruct = pymatgen_structure(lattice, atoms)
pystruct.make_supercell(supercell)
lattice = load_lattice(pystruct)
el = ElementCoulomb(system.atnum)
atoms = [el => [s.frac_coords for s in pystruct.sites]]
end
red_kcoords, _ = bzmesh_uniform(kgrid_size, kshift=kshift)
symmetries = DFTK.symmetry_operations(lattice, atoms)
irred_kcoords, ksymops = bzmesh_ir_wedge(kgrid_size, symmetries; kshift=kshift)
@test length(irred_kcoords) == kirredsize
# Try to reproduce all kcoords from irred_kcoords
all_kcoords = Vector{Vec3{Rational{Int}}}()
for (ik, k) in enumerate(irred_kcoords)
append!(all_kcoords, [S * k for (S, τ) in ksymops[ik]])
end
# Normalize the obtained k-Points and test for equality
red_kcoords = sort([mod.(k .* kgrid_size, kgrid_size) for k in red_kcoords])
all_kcoords = sort([mod.(k .* kgrid_size, kgrid_size) for k in all_kcoords])
@test all_kcoords == red_kcoords
end
test_reduction(silicon, [ 2, 3, 2], 6)
test_reduction(silicon, [ 3, 3, 3], 4)
test_reduction(silicon, [ 2, 3, 4], 14)
test_reduction(silicon, [ 9, 11, 13], 644)
test_reduction(silicon, [ 3, 3, 3], 6, kshift=[1//2, 1//2, 1//2])
test_reduction(silicon, [ 3, 3, 3], 6, kshift=[1//2, 0, 1//2])
test_reduction(silicon, [ 3, 3, 3], 6, kshift=[0, 1//2, 0])
test_reduction(silicon, [ 1, 4, 4], 7, supercell=[2, 1, 1])
test_reduction(silicon, [ 1, 16, 16], 73, supercell=[4, 1, 1])
test_reduction(magnesium, [ 2, 3, 2], 8)
test_reduction(magnesium, [ 3, 3, 3], 6)
test_reduction(magnesium, [ 2, 3, 4], 12)
test_reduction(magnesium, [ 9, 11, 13], 350)
test_reduction(platinum_hcp, [5, 5, 5], 63)
end
@testset "standardize_atoms" begin
# Test unperturbed structure
atoms = [ElementCoulomb(:Si) => silicon.positions]
slattice, satoms = standardize_atoms(silicon.lattice, atoms, primitive=true)
@test length(atoms) == 1
@test atoms[1][1] == ElementCoulomb(:Si)
@test length(atoms[1][2]) == 2
@test atoms[1][2][1] == ones(3) ./ 8
@test atoms[1][2][2] == -ones(3) ./ 8
# Perturb structure
plattice = silicon.lattice .+ 1e-8rand(3, 3)
patoms = [ElementCoulomb(:Si) => [p + 1e-8rand(3) for p in silicon.positions]]
plattice, patoms = standardize_atoms(plattice, patoms, primitive=true)
# And check we get the usual silicon primitive cell back:
a = plattice[1, 2]
@test plattice == [0 a a; a 0 a; a a 0]
@test length(atoms) == 1
@test atoms[1][1] == ElementCoulomb(:Si)
@test length(atoms[1][2]) == 2
@test atoms[1][2][1] - atoms[1][2][2] == ones(3) ./ 4
end
@testset "kgrid_size_from_minimal_spacing" begin
# Test that units are stripped from both the lattice and the spacing
lattice = [[-1 1 1]; [1 -1 1]; [1 1 -1]]
@test kgrid_size_from_minimal_spacing(lattice * u"angstrom", 0.5 / u"angstrom") == [9; 9; 9]
end