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.oncvpsp3.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/1ea71a84cf375286564538a9cab789991f4bf1f4/Si.upf")
ElementPsp(Si, "/home/runner/.julia/artifacts/1ea71a84cf375286564538a9cab789991f4bf1f4/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.
model = model_DFT(system;
functionals=LDA(),
temperature=1e-3,
pseudopotentials=Dict(:Si => "hgh/lda/si-q4"))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, "hgh/lda/si-q4")
ElementPsp(Si, "hgh/lda/si-q4")
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 -7.921721455608 -0.69 6.0 285ms
2 -7.926163562514 -2.35 -1.22 1.0 145ms
3 -7.926839178651 -3.17 -2.37 1.9 182ms
4 -7.926861193323 -4.66 -3.04 2.1 182ms
5 -7.926861651369 -6.34 -3.40 1.9 164ms
6 -7.926861671002 -7.71 -3.82 1.6 167ms
7 -7.926861678461 -8.13 -4.07 1.4 150ms
8 -7.926861681782 -8.48 -4.93 1.2 144ms
9 -7.926861681856 -10.13 -5.15 2.5 171ms
10 -7.926861681871 -10.80 -6.25 1.0 143ms
11 -7.926861681873 -11.91 -6.40 3.2 198ms
12 -7.926861681873 -14.05 -6.37 1.0 143ms
13 -7.926861681873 -14.21 -7.67 1.0 203ms
14 -7.926861681873 -15.05 -7.63 3.4 191ms
15 -7.926861681873 + -14.75 -8.60 1.0 144msIf 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 = Dict(:Si => "hgh/lda/si-q4")
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 -7.921743422828 -0.69 6.0 233ms
2 -7.926165394398 -2.35 -1.22 1.0 146ms
3 -7.926838074160 -3.17 -2.37 1.9 197ms
4 -7.926861186185 -4.64 -3.03 2.1 182ms
5 -7.926861642948 -6.34 -3.37 1.9 164ms
6 -7.926861667020 -7.62 -3.73 1.5 152ms
7 -7.926861678827 -7.93 -4.09 1.2 146ms
8 -7.926861681798 -8.53 -5.10 1.6 156ms
9 -7.926861681861 -10.20 -5.21 2.5 214ms
10 -7.926861681872 -10.96 -6.40 1.0 142ms
11 -7.926861681873 -12.23 -6.60 3.1 195ms
12 -7.926861681873 -14.27 -6.74 1.1 145ms
13 -7.926861681873 -14.75 -7.93 1.0 143ms
14 -7.926861681873 -14.75 -8.74 3.0 190msThe 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 = Dict(:Si => "hgh/lda/si-q4")
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 -7.921724304318 -0.69 6.0 267ms
2 -7.926168723131 -2.35 -1.22 1.0 157ms
3 -7.926841594910 -3.17 -2.37 1.9 169ms
4 -7.926864612033 -4.64 -3.01 2.1 193ms
5 -7.926865043171 -6.37 -3.32 1.9 166ms
6 -7.926865073563 -7.52 -3.66 1.5 176ms
7 -7.926865090702 -7.77 -4.18 1.2 134msObtaining 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, 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, 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")