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 -7.921728328688 -0.69 5.9 224ms
2 -7.926165571315 -2.35 -1.22 1.0 157ms
3 -7.926838914180 -3.17 -2.37 1.9 203ms
4 -7.926861197652 -4.65 -3.03 2.2 269ms
5 -7.926861647829 -6.35 -3.39 2.1 174ms
6 -7.926861668345 -7.69 -3.76 1.6 157ms
7 -7.926861678631 -7.99 -4.07 1.2 150ms
8 -7.926861681784 -8.50 -5.00 1.6 158ms
9 -7.926861681858 -10.13 -5.17 3.0 215ms
10 -7.926861681872 -10.86 -6.34 1.0 161ms
11 -7.926861681873 -12.09 -6.49 3.0 205ms
12 -7.926861681873 -14.21 -7.39 1.0 153ms
┌ Warning: Eigensolver not converged
│ n_iter =
│ 8-element Vector{Int64}:
│ 3
│ 2
│ 2
│ 2
│ 2
│ 3
│ 2
│ 3
└ @ DFTK ~/work/DFTK.jl/DFTK.jl/src/scf/self_consistent_field.jl:76
13 -7.926861681873 -14.75 -7.46 2.4 217ms
14 -7.926861681873 + -15.05 -7.75 1.0 152ms
15 -7.926861681873 + -Inf -9.32 1.1 287msIf 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 -7.921731818733 -0.69 5.9 251ms
2 -7.926163308194 -2.35 -1.22 1.0 181ms
3 -7.926838429207 -3.17 -2.37 1.9 221ms
4 -7.926861210646 -4.64 -3.02 2.1 218ms
5 -7.926861637625 -6.37 -3.34 1.9 718ms
6 -7.926861664105 -7.58 -3.68 1.5 151ms
7 -7.926861679602 -7.81 -4.18 1.1 147ms
8 -7.926861681807 -8.66 -5.20 1.8 156ms
9 -7.926861681863 -10.25 -5.22 3.2 190ms
10 -7.926861681872 -11.02 -6.51 1.0 143ms
11 -7.926861681873 -12.40 -6.78 3.0 602ms
12 -7.926861681873 -14.75 -7.22 1.2 150ms
13 -7.926861681873 -14.75 -7.91 1.2 148ms
┌ 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
14 -7.926861681873 + -15.05 -8.55 2.4 177msThe 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 -7.921727148106 -0.69 5.9 266ms
2 -7.926166107149 -2.35 -1.22 1.0 159ms
3 -7.926842576541 -3.17 -2.37 1.9 182ms
4 -7.926864635414 -4.66 -3.03 2.1 206ms
5 -7.926865057874 -6.37 -3.38 1.9 172ms
6 -7.926865079219 -7.67 -3.75 1.5 155ms
7 -7.926865090563 -7.95 -4.16 1.1 148msObtaining 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