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 -7.921724495937 -0.69 6.0 301ms
2 -7.926164046667 -2.35 -1.22 1.0 204ms
3 -7.926839164153 -3.17 -2.37 1.9 201ms
4 -7.926861182278 -4.66 -3.04 2.1 224ms
5 -7.926861650764 -6.33 -3.41 1.9 199ms
6 -7.926861670497 -7.70 -3.81 1.5 197ms
7 -7.926861678713 -8.09 -4.09 1.4 182ms
8 -7.926861681794 -8.51 -5.00 1.4 183ms
9 -7.926861681861 -10.18 -5.24 2.8 216ms
10 -7.926861681872 -10.97 -6.30 1.1 178ms
11 -7.926861681873 -12.06 -6.53 2.9 230ms
12 -7.926861681873 -14.35 -6.53 1.1 179ms
13 -7.926861681873 -14.75 -7.56 1.0 176ms
14 -7.926861681873 -14.75 -7.75 2.4 213ms
15 -7.926861681873 -15.05 -8.79 1.1 194msIf 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 -7.921709782408 -0.69 5.9 299ms
2 -7.926166022236 -2.35 -1.22 1.0 201ms
3 -7.926839331971 -3.17 -2.37 1.9 218ms
4 -7.926861203061 -4.66 -3.04 2.2 230ms
5 -7.926861649907 -6.35 -3.40 2.0 242ms
6 -7.926861669494 -7.71 -3.78 1.5 192ms
7 -7.926861678637 -8.04 -4.08 1.6 197ms
8 -7.926861681796 -8.50 -5.01 1.1 188ms
9 -7.926861681860 -10.19 -5.23 3.1 235ms
10 -7.926861681872 -10.95 -6.26 1.0 227ms
11 -7.926861681873 -12.01 -6.56 2.5 239ms
12 -7.926861681873 -14.35 -6.60 1.2 192ms
13 -7.926861681873 -14.45 -7.55 1.0 183ms
14 -7.926861681873 + -Inf -7.67 2.5 226ms
15 -7.926861681873 + -15.05 -8.78 1.0 234msThe 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 -7.921729327372 -0.69 5.9 318ms
2 -7.926166726889 -2.35 -1.22 1.0 202ms
3 -7.926843212869 -3.17 -2.37 1.9 215ms
4 -7.926864637666 -4.67 -3.05 2.2 247ms
5 -7.926865066489 -6.37 -3.43 1.9 210ms
6 -7.926865083113 -7.78 -3.84 1.6 196ms
7 -7.926865089611 -8.19 -4.06 1.5 189msObtaining 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