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, periodicity = TTT):
cell_vectors : [ 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")
By default the atoms of an AbstractSystem employ the bare Coulomb potential. To employ pseudpotential models (which is almost always advisable for plane-wave DFT) one employs the pseudopotential keyword argument in model constructors such as model_DFT. For example we can employ a PseudoFamily object from the PseudoPotentialData package. See its documentation for more information on the available pseudopotential families and how to select them.
using PseudoPotentialData # defines PseudoFamily
pd_lda_family = PseudoFamily("dojo.nc.sr.lda.v0_4_1.standard.upf")
model = model_DFT(system; functionals=LDA(), temperature=1e-3,
pseudopotentials=pd_lda_family)Model(lda_x+lda_c_pw, 3D):
lattice (in Bohr) : [0 , 5.13061 , 5.13061 ]
[5.13061 , 0 , 5.13061 ]
[5.13061 , 5.13061 , 0 ]
unit cell volume : 270.11 Bohr³
atoms : Si₂
atom potentials : ElementPsp(Si, "/home/runner/.julia/artifacts/326db5c901e2681584ec5c06fc17f6c96e516ff9/Si.upf")
ElementPsp(Si, "/home/runner/.julia/artifacts/326db5c901e2681584ec5c06fc17f6c96e516ff9/Si.upf")
num. electrons : 8
spin polarization : none
temperature : 0.001 Ha
smearing : DFTK.Smearing.FermiDirac()
terms : Kinetic()
AtomicLocal()
AtomicNonlocal()
Ewald(nothing)
PspCorrection()
Hartree()
Xc(lda_x, lda_c_pw)
Entropy()Alternatively the pseudopotentials object also accepts a Dict{Symbol,String}, which provides for each element symbol the filename or identifier of the pseudopotential to be employed, e.g.
path_to_pspfile = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")[:Si]
model = model_DFT(system; functionals=LDA(), temperature=1e-3,
pseudopotentials=Dict(:Si => path_to_pspfile))Model(lda_x+lda_c_pw, 3D):
lattice (in Bohr) : [0 , 5.13061 , 5.13061 ]
[5.13061 , 0 , 5.13061 ]
[5.13061 , 5.13061 , 0 ]
unit cell volume : 270.11 Bohr³
atoms : Si₂
atom potentials : ElementPsp(Si, "/home/runner/.julia/artifacts/966fd9cdcd7dbaba6dc2bf43ee50dd81e63e8837/Si.gth")
ElementPsp(Si, "/home/runner/.julia/artifacts/966fd9cdcd7dbaba6dc2bf43ee50dd81e63e8837/Si.gth")
num. electrons : 8
spin polarization : none
temperature : 0.001 Ha
smearing : DFTK.Smearing.FermiDirac()
terms : Kinetic()
AtomicLocal()
AtomicNonlocal()
Ewald(nothing)
PspCorrection()
Hartree()
Xc(lda_x, lda_c_pw)
Entropy()We can then discretise such a model and solve:
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 -7.921738493167 -0.69 5.8 220ms
2 -7.926134152303 -2.36 -1.22 1.0 136ms
3 -7.926833989759 -3.16 -2.37 2.1 175ms
4 -7.926861266375 -4.56 -3.02 2.9 200ms
5 -7.926861654220 -6.41 -3.45 2.2 202ms
6 -7.926861674359 -7.70 -3.98 1.6 156ms
7 -7.926861678116 -8.43 -4.06 1.8 160ms
8 -7.926861679773 -8.78 -4.18 1.0 142ms
9 -7.926861681796 -8.69 -4.71 1.0 146ms
10 -7.926861681854 -10.24 -4.87 1.4 154ms
11 -7.926861681867 -10.87 -5.13 1.2 155ms
12 -7.926861681872 -11.32 -6.13 1.1 181ms
13 -7.926861681873 -12.30 -6.59 2.6 183ms
14 -7.926861681873 -13.97 -6.17 1.5 157ms
15 -7.926861681873 -13.85 -7.09 1.0 148ms
16 -7.926861681873 + -15.05 -6.79 1.0 150ms
17 -7.926861681873 + -14.57 -8.19 1.0 146msIf we did not want to use AtomsBuilder we could of course use any other package which yields an AbstractSystem object. This includes:
Reading a system using AtomsIO
Read a file using AtomsIO, which directly yields an AbstractSystem.
using AtomsIO
system = load_system("Si.extxyz");Run the LDA calculation:
pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")
model = model_DFT(system; pseudopotentials, 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 -7.921711284492 -0.69 5.5 194ms
2 -7.926134221601 -2.35 -1.22 1.0 141ms
3 -7.926833369669 -3.16 -2.37 2.0 163ms
4 -7.926861262875 -4.55 -2.99 3.1 203ms
5 -7.926861648486 -6.41 -3.40 2.1 170ms
6 -7.926861671712 -7.63 -3.88 1.4 152ms
7 -7.926861679157 -8.13 -4.14 1.9 201ms
8 -7.926861681784 -8.58 -4.91 1.2 147ms
9 -7.926861681847 -10.20 -5.10 2.4 181ms
10 -7.926861681865 -10.74 -5.49 1.2 153ms
11 -7.926861681872 -11.16 -6.25 1.2 154ms
12 -7.926861681873 -12.52 -6.95 2.5 186ms
13 -7.926861681873 -14.21 -7.18 2.4 209ms
14 -7.926861681873 -14.57 -8.15 1.0 148msThe 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:
pseudopotentials = PseudoFamily("cp2k.nc.sr.lda.v0_1.semicore.gth")
model = model_DFT(system; pseudopotentials, 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 -7.921718050805 -0.69 5.6 221ms
2 -7.926135936654 -2.35 -1.22 1.0 141ms
3 -7.926837435886 -3.15 -2.37 2.0 151ms
4 -7.926864456678 -4.57 -3.01 3.1 219ms
5 -7.926865072793 -6.21 -3.44 2.0 179ms
6 -7.926865086290 -7.87 -4.01 1.4 140msObtaining 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, periodicity = TTT):
cell_vectors : [ 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")
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, pseudopotentials)
atoms = [Si, Si]
positions = [ones(3)/8, -ones(3)/8]
third_system = atomic_system(lattice, atoms, positions)FlexibleSystem(Si₂, periodicity = TTT):
cell_vectors : [ 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")