AtomsBase integration
AtomsBase.jl is a common interface for representing atomic structures in Julia. DFTK directly supports using such structures to run a calculation as is demonstrated here.
using DFTKFeeding an AtomsBase AbstractSystem to DFTK
In this example we construct a silicon system using the ase.build.bulk routine from the atomistic simulation environment (ASE), which is exposed by ASEconvert as an AtomsBase AbstractSystem.
# Construct bulk system and convert to an AbstractSystem
using ASEconvert
system_ase = ase.build.bulk("Si")
system = pyconvert(AbstractSystem, system_ase)FlexibleSystem(Si₂, periodic = TTT):
bounding_box : [ 0 2.715 2.715;
2.715 0 2.715;
2.715 2.715 0]u"Å"
Atom(Si, [ 0, 0, 0]u"Å")
Atom(Si, [ 1.3575, 1.3575, 1.3575]u"Å")
Si
Si
To use an AbstractSystem in DFTK, we attach pseudopotentials, construct a DFT model, discretise and solve:
system = attach_psp(system; Si="hgh/lda/si-q4")
model = model_LDA(system; temperature=1e-3)
basis = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
scfres = self_consistent_field(basis, tol=1e-8);n Energy log10(ΔE) log10(Δρ) Diag Δtime
--- --------------- --------- --------- ---- ------
1 -7.921726940924 -0.69 6.0 264ms
2 -7.926163938443 -2.35 -1.22 1.0 177ms
3 -7.926839352954 -3.17 -2.37 1.9 182ms
4 -7.926861193446 -4.66 -3.03 2.2 235ms
5 -7.926861644956 -6.35 -3.38 2.0 179ms
6 -7.926861667119 -7.65 -3.73 1.5 176ms
7 -7.926861678835 -7.93 -4.10 1.1 155ms
8 -7.926861681798 -8.53 -5.08 1.8 164ms
9 -7.926861681861 -10.20 -5.21 2.6 192ms
10 -7.926861681872 -10.95 -6.37 1.0 200ms
11 -7.926861681873 -12.22 -6.56 3.1 212ms
12 -7.926861681873 -14.15 -7.47 1.0 154ms
┌ Warning: Eigensolver not converged
│ n_iter =
│ 8-element Vector{Int64}:
│ 2
│ 2
│ 3
│ 2
│ 2
│ 3
│ 2
│ 3
└ @ DFTK ~/work/DFTK.jl/DFTK.jl/src/scf/self_consistent_field.jl:76
13 -7.926861681873 -15.05 -7.61 2.4 197ms
┌ Warning: Eigensolver not converged
│ n_iter =
│ 8-element Vector{Int64}:
│ 1
│ 1
│ 1
│ 1
│ 1
│ 1
│ 1
│ 1
└ @ DFTK ~/work/DFTK.jl/DFTK.jl/src/scf/self_consistent_field.jl:76
14 -7.926861681873 + -14.75 -8.81 1.0 159msIf we did not want to use ASE we could of course use any other package which yields an AbstractSystem object. This includes:
Reading a system using AtomsIO
using AtomsIO
# Read a file using [AtomsIO](https://github.com/mfherbst/AtomsIO.jl),
# which directly yields an AbstractSystem.
system = load_system("Si.extxyz")
# Now run the LDA calculation:
system = attach_psp(system; Si="hgh/lda/si-q4")
model = model_LDA(system; temperature=1e-3)
basis = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
scfres = self_consistent_field(basis, tol=1e-8);n Energy log10(ΔE) log10(Δρ) Diag Δtime
--- --------------- --------- --------- ---- ------
1 -7.921733930539 -0.69 6.1 246ms
2 -7.926162604463 -2.35 -1.22 1.0 157ms
3 -7.926836774341 -3.17 -2.37 1.9 180ms
4 -7.926861164586 -4.61 -3.02 2.1 213ms
5 -7.926861643559 -6.32 -3.37 1.8 216ms
6 -7.926861667469 -7.62 -3.74 1.6 159ms
7 -7.926861678708 -7.95 -4.08 1.2 152ms
8 -7.926861681788 -8.51 -5.05 1.6 161ms
9 -7.926861681859 -10.14 -5.18 2.8 196ms
10 -7.926861681872 -10.89 -6.25 1.0 151ms
11 -7.926861681873 -12.22 -6.56 2.9 260ms
12 -7.926861681873 -14.05 -7.28 1.0 151ms
13 -7.926861681873 -14.75 -7.74 2.5 188ms
14 -7.926861681873 -14.75 -7.84 1.8 167ms
15 -7.926861681873 + -14.57 -8.78 1.0 155msThe same could be achieved using ExtXYZ by system = Atoms(read_frame("Si.extxyz")), since the ExtXYZ.Atoms object is directly AtomsBase-compatible.
Directly setting up a system in AtomsBase
using AtomsBase
using Unitful
using UnitfulAtomic
# Construct a system in the AtomsBase world
a = 10.26u"bohr" # Silicon lattice constant
lattice = a / 2 * [[0, 1, 1.], # Lattice as vector of vectors
[1, 0, 1.],
[1, 1, 0.]]
atoms = [:Si => ones(3)/8, :Si => -ones(3)/8]
system = periodic_system(atoms, lattice; fractional=true)
# Now run the LDA calculation:
system = attach_psp(system; Si="hgh/lda/si-q4")
model = model_LDA(system; temperature=1e-3)
basis = PlaneWaveBasis(model; Ecut=15, kgrid=[4, 4, 4])
scfres = self_consistent_field(basis, tol=1e-4);n Energy log10(ΔE) log10(Δρ) Diag Δtime
--- --------------- --------- --------- ---- ------
1 -7.921732627560 -0.69 5.9 331ms
2 -7.926166544697 -2.35 -1.22 1.0 166ms
3 -7.926842166695 -3.17 -2.37 1.9 196ms
4 -7.926864593850 -4.65 -3.03 2.1 216ms
5 -7.926865060563 -6.33 -3.39 1.9 198ms
6 -7.926865081030 -7.69 -3.79 1.5 174ms
7 -7.926865089688 -8.06 -4.07 1.4 162msObtaining an AbstractSystem from DFTK data
At any point we can also get back the DFTK model as an AtomsBase-compatible AbstractSystem:
second_system = atomic_system(model)FlexibleSystem(Si₂, periodic = TTT):
bounding_box : [ 0 5.13 5.13;
5.13 0 5.13;
5.13 5.13 0]u"a₀"
Atom(Si, [ 1.2825, 1.2825, 1.2825]u"a₀")
Atom(Si, [ -1.2825, -1.2825, -1.2825]u"a₀")
Si
Si
Similarly DFTK offers a method to the atomic_system and periodic_system functions (from AtomsBase), which enable a seamless conversion of the usual data structures for setting up DFTK calculations into an AbstractSystem:
lattice = 5.431u"Å" / 2 * [[0 1 1.];
[1 0 1.];
[1 1 0.]];
Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
atoms = [Si, Si]
positions = [ones(3)/8, -ones(3)/8]
third_system = atomic_system(lattice, atoms, positions)FlexibleSystem(Si₂, periodic = TTT):
bounding_box : [ 0 5.13155 5.13155;
5.13155 0 5.13155;
5.13155 5.13155 0]u"a₀"
Atom(Si, [ 1.28289, 1.28289, 1.28289]u"a₀")
Atom(Si, [-1.28289, -1.28289, -1.28289]u"a₀")
Si
Si