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
pseudopot. family : PseudoFamily("dojo.nc.sr.lda.v0_4_1.standard.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 -7.921706860692 -0.69 5.5 206ms
2 -7.926134460772 -2.35 -1.22 1.0 222ms
3 -7.926833730117 -3.16 -2.37 2.0 167ms
4 -7.926861256511 -4.56 -3.01 3.0 220ms
5 -7.926861656091 -6.40 -3.45 2.0 177ms
6 -7.926861674335 -7.74 -4.01 1.6 167ms
7 -7.926861678283 -8.40 -4.07 1.9 167ms
8 -7.926861679228 -9.02 -4.15 1.0 152ms
9 -7.926861681775 -8.59 -4.58 1.0 155ms
10 -7.926861681850 -10.12 -4.80 1.0 151ms
11 -7.926861681866 -10.77 -5.46 1.2 157ms
12 -7.926861681871 -11.30 -5.70 2.1 180ms
13 -7.926861681872 -12.02 -5.87 1.1 155ms
14 -7.926861681873 -12.95 -6.14 1.0 154ms
15 -7.926861681873 -13.38 -6.64 1.1 156ms
16 -7.926861681873 -14.21 -7.40 1.9 167ms
17 -7.926861681873 -14.75 -7.47 2.2 190ms
18 -7.926861681873 + -Inf -8.43 1.0 155msIf 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 -7.921740083263 -0.69 5.6 235ms
2 -7.926132157578 -2.36 -1.22 1.0 149ms
3 -7.926834110851 -3.15 -2.37 2.0 176ms
4 -7.926861243774 -4.57 -3.02 3.0 208ms
5 -7.926861658503 -6.38 -3.48 2.1 180ms
6 -7.926861676171 -7.75 -4.07 1.9 169ms
7 -7.926861678639 -8.61 -4.11 1.9 174ms
8 -7.926861678789 -9.82 -4.13 1.0 148ms
9 -7.926861681435 -8.58 -3.97 1.0 153ms
10 -7.926861681823 -9.41 -4.44 1.0 150ms
11 -7.926861681793 + -10.52 -4.35 1.0 156ms
12 -7.926861681812 -10.73 -4.39 1.0 152ms
13 -7.926861681863 -10.30 -4.76 1.0 149ms
14 -7.926861681868 -11.29 -4.88 1.0 158ms
15 -7.926861681872 -11.44 -5.13 1.0 154ms
16 -7.926861681871 + -12.13 -5.06 1.0 149ms
17 -7.926861681872 -11.77 -5.53 1.0 160ms
18 -7.926861681873 -13.44 -5.56 1.0 154ms
19 -7.926861681873 -13.15 -5.92 1.0 149ms
20 -7.926861681872 + -12.87 -5.80 1.2 161ms
21 -7.926861681873 -12.79 -6.30 1.0 154ms
22 -7.926861681873 -13.80 -7.10 1.1 153ms
23 -7.926861681873 + -14.75 -8.11 1.9 172msThe 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 -7.921729591529 -0.69 5.5 227ms
2 -7.926134269916 -2.36 -1.22 1.0 155ms
3 -7.926838065454 -3.15 -2.37 2.0 157ms
4 -7.926864652754 -4.58 -3.03 3.0 206ms
5 -7.926865071033 -6.38 -3.48 2.1 169ms
6 -7.926865086749 -7.80 -4.09 1.5 139msObtaining 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")