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 DFTK
using AtomsBuilderFeeding an AtomsBase AbstractSystem to DFTK
In this example we construct a bulk silicon system using the bulk function from AtomsBuilder. This function uses tabulated data to set up a reasonable starting geometry and lattice for bulk silicon.
system = bulk(:Si)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
By default the atoms of an AbstractSystem employ the bare Coulomb potential. To make calculations feasible for plane-wave DFT we thus attach pseudopotential information, before passing the system to construct a DFT model, discretise and solve:
system = attach_psp(system; Si="hgh/lda/si-q4")
model = model_DFT(system; functionals=LDA(), 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 -7.921726746289 -0.69 6.0 256ms
2 -7.926164308317 -2.35 -1.22 1.0 155ms
3 -7.926839237591 -3.17 -2.37 1.9 176ms
4 -7.926861199790 -4.66 -3.04 2.1 189ms
5 -7.926861652648 -6.34 -3.41 2.0 171ms
6 -7.926861671100 -7.73 -3.82 1.6 206ms
7 -7.926861678324 -8.14 -4.05 1.1 149ms
8 -7.926861681780 -8.46 -4.88 1.4 154ms
9 -7.926861681858 -10.11 -5.18 2.8 183ms
10 -7.926861681872 -10.86 -6.19 1.5 158ms
11 -7.926861681873 -11.98 -6.43 2.9 198ms
12 -7.926861681873 -14.21 -6.28 1.0 150ms
13 -7.926861681873 -14.35 -7.35 1.0 148ms
14 -7.926861681873 + -15.05 -7.47 2.5 184ms
15 -7.926861681873 -14.35 -8.56 1.0 152msIf 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_DFT(system; functionals=LDA(), 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 -7.921712243822 -0.69 6.0 232ms
2 -7.926163011018 -2.35 -1.22 1.0 157ms
3 -7.926838940325 -3.17 -2.37 2.0 182ms
4 -7.926861252050 -4.65 -3.03 2.0 186ms
5 -7.926861648028 -6.40 -3.39 1.9 169ms
6 -7.926861668698 -7.68 -3.76 1.6 170ms
7 -7.926861679070 -7.98 -4.12 1.1 149ms
8 -7.926861681795 -8.56 -5.11 1.8 185ms
9 -7.926861681855 -10.22 -5.14 3.0 198ms
10 -7.926861681872 -10.77 -6.29 1.0 149ms
11 -7.926861681873 -12.13 -6.54 2.8 257ms
12 -7.926861681873 -14.05 -6.94 1.0 173ms
13 -7.926861681873 + -15.05 -7.61 1.6 186ms
14 -7.926861681873 -14.57 -8.25 2.9 272msThe 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_DFT(system; functionals=LDA(), 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 -7.921715946320 -0.69 6.0 409ms
2 -7.926169061291 -2.35 -1.22 1.0 190ms
3 -7.926842414158 -3.17 -2.37 1.9 250ms
4 -7.926864609915 -4.65 -3.02 2.1 260ms
5 -7.926865049611 -6.36 -3.34 1.9 230ms
6 -7.926865075274 -7.59 -3.68 1.5 190ms
7 -7.926865090567 -7.82 -4.16 1.0 175msObtaining 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