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Update to DFTK 0.7.6 (#28)
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@Technici4n
Technici4n authored Jan 13, 2025
1 parent ffa0d98 commit 78d22ac
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4 changes: 2 additions & 2 deletions Project.toml
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Expand Up @@ -21,8 +21,8 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"

[compat]
AtomsBase = "0.3"
DFTK = "0.6.20"
AtomsBase = "0.5"
DFTK = "0.7.6"
DocStringExtensions = "0.9"
HDF5 = "0.17"
JLD2 = "0.4, 0.5"
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9 changes: 5 additions & 4 deletions precompilation_task.json
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Expand Up @@ -24,20 +24,21 @@
1.282887730510825,
1.282887730510825,
1.282887730510825
],
"pseudopotential": "hgh/lda/si-q4"
]
},
{
"symbol": "Si",
"position": [
-1.282887730510825,
-1.282887730510825,
-1.282887730510825
],
"pseudopotential": "hgh/lda/si-q4"
]
}
]
},
"pseudopotentials": {
"Si": "hgh/lda/si-q4"
},
"model_kwargs": {
"functionals": [
":lda_x",
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20 changes: 15 additions & 5 deletions src/AiidaDFTK.jl
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Expand Up @@ -36,20 +36,30 @@ function build_system(data)
atoms = map(data["periodic_system"]["atoms"]) do atom
symbol = Symbol(atom["symbol"])
position = convert(Vector{Float64}, atom["position"]) * u"bohr"
pseudopotential = atom["pseudopotential"]
pseudopotential_kwargs = parse_kwargs(get(atom, "pseudopotential_kwargs", Dict()))
magnetic_moment = convert(Float64, get(atom, "magnetic_moment", 0.0))
Atom(symbol, position; pseudopotential, pseudopotential_kwargs, magnetic_moment)
Atom(symbol, position; magnetic_moment)
end

bounding_box = convert(Vector{Vector{Float64}},
data["periodic_system"]["bounding_box"]) * u"bohr"
periodic_system(atoms, bounding_box)
end

function build_pseudopotentials(pseudo_data, system)
kwargs = parse_kwargs(get(pseudo_data, Symbol("\$kwargs"), Dict()))
family = Dict{Symbol, String}(k => pseudo_data[k]
for k in keys(pseudo_data)
if k != Symbol("\$kwargs"))
load_psp(family, system; kwargs...)
end

function build_basis(data, system)
model = model_DFT(system; parse_kwargs(data["model_kwargs"])...)
PlaneWaveBasis(model; parse_kwargs(data["basis_kwargs"])...)
pseudopotentials = build_pseudopotentials(data["pseudopotentials"], system)
parsed = DFTK.parse_system(system, pseudopotentials)
model = model_DFT(parsed.lattice, parsed.atoms, parsed.positions;
parsed.magnetic_moments,
parse_kwargs(data["model_kwargs"])...)
PlaneWaveBasis(model; parse_kwargs(data["basis_kwargs"])...)
end

function run_geometry_optimisation(data, system, basis)
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10 changes: 6 additions & 4 deletions test/iron.json
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Expand Up @@ -25,14 +25,16 @@
0,
0
],
"pseudopotential": "../Fe.upf",
"pseudopotential_kwargs": {
"rcut": 10
},
"magnetic_moment": 4
}
]
},
"pseudopotentials": {
"Fe": "../Fe.upf",
"$kwargs": {
"rcut": 10
}
},
"model_kwargs": {
"functionals": [
":gga_x_pbe",
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46 changes: 31 additions & 15 deletions test/runtests.jl
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Expand Up @@ -12,21 +12,15 @@ using UnitfulAtomic
@testset "AiidaDFTK.jl" begin
system_silicon = periodic_system(
[Atom(:Si, [ 1.28, 1.28, 1.28]u"bohr";
pseudopotential="hgh/lda/si-q4",
pseudopotential_kwargs=Dict(),
magnetic_moment=0.0),
Atom(:Si, [-1.28, -1.28, -1.28]u"bohr";
pseudopotential="hgh/lda/si-q4",
pseudopotential_kwargs=Dict(),
magnetic_moment=0.0)],
[[0.0, 5.13, 5.13],
[5.13, 0.0, 5.13],
[5.13, 5.13, 0.0]]u"bohr"
)
system_iron = periodic_system(
[Atom(:Fe, [0, 0, 0]u"bohr";
pseudopotential="Fe.upf",
pseudopotential_kwargs=Dict(:rcut => 10, ),
magnetic_moment=4.0)],
[[-2.711, 2.711, 2.711],
[ 2.711, -2.711, 2.711],
Expand Down Expand Up @@ -61,42 +55,62 @@ using UnitfulAtomic
[5.13, 0.0, 5.13],
[5.13, 5.13, 0.0]],
"atoms" => [Dict("symbol" => "Si",
"position" => [1.28, 1.28, 1.28],
"pseudopotential" => "hgh/lda/si-q4"),
"position" => [1.28, 1.28, 1.28]),
Dict("symbol" => "Si",
"position" => [-1.28, -1.28, -1.28],
"pseudopotential" => "hgh/lda/si-q4")])
"position" => [-1.28, -1.28, -1.28])],)

res = AiidaDFTK.build_system(Dict("periodic_system" => data))
test_approx_eq(res, system_silicon)
end

@testset "build_system iron" begin
pseudo = Dict("rcut" => 10, )
data = Dict("bounding_box" => [[-2.711, 2.711, 2.711],
[ 2.711, -2.711, 2.711],
[ 2.711, 2.711, -2.711]],
"atoms" => [Dict("symbol" => "Fe",
"position" => [0, 0, 0],
"pseudopotential" => "Fe.upf",
"magnetic_moment" => 4.0,
"pseudopotential_kwargs" => pseudo,
)])
res = AiidaDFTK.build_system(Dict("periodic_system" => data))
test_approx_eq(res, system_iron)
end


@testset "build_pseudopotentials silicon" begin
pseudo_data = Dict(:Si => "hgh/lda/si-q4")
pseudos = AiidaDFTK.build_pseudopotentials(pseudo_data, system_silicon)

@test length(pseudos) == 2
@test pseudos[1] == pseudos[2]
@test pseudos[1] isa PspHgh
end

@testset "build_pseudopotentials iron" begin
pseudo_data = Dict(:Fe => "Fe.upf",
Symbol("\$kwargs") => Dict("rcut" => 10))
pseudos = AiidaDFTK.build_pseudopotentials(pseudo_data, system_iron)

@test length(pseudos) == 1
@test pseudos[1] isa PspUpf
@test pseudos[1].rcut == 10
end

@testset "build_basis silicon" begin
smearing = Dict("\$symbol" => "Smearing.MethfesselPaxton", "\$args" => [1])
data = Dict(
"pseudopotentials" => Dict(:Si => "hgh/lda/si-q4"),
"model_kwargs" => Dict("functionals" => [":lda_x", ":lda_c_pw"],
"temperature" => 1e-3,
"smearing" => smearing),
"basis_kwargs" => Dict("kgrid" => [4, 4, 4], "Ecut" => 15),
)
basis = AiidaDFTK.build_basis(data, system_silicon)

ref_model = model_DFT(system_silicon, [:lda_x, :lda_c_pw];
temperature=1e-3, smearing=Smearing.MethfesselPaxton(1))
ref_pseudos = repeat([load_psp("hgh/lda/si-q4")], 2)
ref_model = model_DFT(system_silicon;
functionals=[:lda_x, :lda_c_pw],
temperature=1e-3, smearing=Smearing.MethfesselPaxton(1),
pseudopotentials=ref_pseudos)
ref_basis = PlaneWaveBasis(ref_model; kgrid=[4, 4, 4], Ecut=15)

# TODO Add == implementation for models to DFTK
Expand Down Expand Up @@ -124,6 +138,8 @@ using UnitfulAtomic

smearing = Dict("\$symbol" => "Smearing.MarzariVanderbilt")
data = Dict(
"pseudopotentials" => Dict(:Fe => "Fe.upf",
Symbol("\$kwargs") => Dict("rcut" => 10)),
"model_kwargs" => Dict("functionals" => [":gga_x_pbe", ":gga_c_pbe"],
"temperature" => 1e-2,
"smearing" => smearing),
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9 changes: 5 additions & 4 deletions test/silicon_bands.json
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Expand Up @@ -24,20 +24,21 @@
1.282887730510825,
1.282887730510825,
1.282887730510825
],
"pseudopotential": "hgh/lda/si-q4"
]
},
{
"symbol": "Si",
"position": [
-1.282887730510825,
-1.282887730510825,
-1.282887730510825
],
"pseudopotential": "hgh/lda/si-q4"
]
}
]
},
"pseudopotentials": {
"Si": "hgh/lda/si-q4"
},
"model_kwargs": {
"functionals": [
":lda_x",
Expand Down

6 comments on commit 78d22ac

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Error while trying to register: Changing package repo URL not allowed, please submit a pull request with the URL change to the target registry and retry.

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Registration pull request created: JuliaRegistries/General/122971

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

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Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.2.0 -m "<description of version>" 78d22ac1495f72cb11e9e2cd46e738cd79ddd624
git push origin v0.2.0

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Release notes:

Breaking changes

  • Changes to the input file format wrt. pseudopotentials.
  • Update to DFTK 0.7.6.
  • Exports were removed.

Other changes

  • Logging file with error messages that can be parsed to detect success and failure.

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Registration pull request updated: JuliaRegistries/General/122971

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.2.0 -m "<description of version>" 78d22ac1495f72cb11e9e2cd46e738cd79ddd624
git push origin v0.2.0

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