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.
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 -7.921732207040 -0.69 5.8 223ms
2 -7.926136080833 -2.36 -1.22 1.0 133ms
3 -7.926833930419 -3.16 -2.37 2.0 176ms
4 -7.926861299567 -4.56 -3.01 2.9 214ms
5 -7.926861653782 -6.45 -3.43 2.1 160ms
6 -7.926861673921 -7.70 -3.95 1.6 147ms
7 -7.926861678961 -8.30 -4.12 2.1 153ms
8 -7.926861681732 -8.56 -4.77 1.2 140ms
9 -7.926861681848 -9.93 -5.12 1.9 152ms
10 -7.926861681871 -10.65 -5.88 1.5 151ms
11 -7.926861681873 -11.76 -6.18 2.5 177ms
12 -7.926861681873 -13.11 -6.64 1.0 140ms
13 -7.926861681873 -14.21 -7.15 2.0 158ms
14 -7.926861681873 -14.75 -7.21 2.1 171ms
15 -7.926861681873 -14.75 -7.83 1.2 148ms
16 -7.926861681873 + -14.57 -8.80 1.5 154msIf 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 -7.921732016371 -0.69 5.6 196ms
2 -7.926136322317 -2.36 -1.22 1.0 133ms
3 -7.926834383951 -3.16 -2.37 2.0 158ms
4 -7.926861263248 -4.57 -3.01 3.0 820ms
5 -7.926861654771 -6.41 -3.43 2.1 164ms
6 -7.926861673602 -7.73 -3.95 1.5 144ms
7 -7.926861678706 -8.29 -4.10 1.9 153ms
8 -7.926861681682 -8.53 -4.62 1.0 159ms
9 -7.926861681838 -9.81 -4.99 1.8 222ms
10 -7.926861681870 -10.51 -5.83 1.5 169ms
11 -7.926861681872 -11.53 -5.97 2.6 183ms
12 -7.926861681873 -12.97 -6.43 1.0 135ms
13 -7.926861681873 -13.69 -6.90 1.4 138ms
14 -7.926861681873 + -Inf -7.31 1.9 157ms
15 -7.926861681873 + -15.05 -8.03 1.5 142msThe 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 -7.921741629155 -0.69 5.5 231ms
2 -7.926135922906 -2.36 -1.22 1.0 123ms
3 -7.926836420259 -3.15 -2.37 2.0 160ms
4 -7.926864669845 -4.55 -2.99 3.0 191ms
5 -7.926865055460 -6.41 -3.37 2.1 155ms
6 -7.926865080963 -7.59 -3.81 1.4 149ms
7 -7.926865090794 -8.01 -4.19 1.4 131msObtaining 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")