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 -7.921713010550 -0.69 5.6 258ms
2 -7.926131207001 -2.35 -1.22 1.0 224ms
3 -7.926834032617 -3.15 -2.37 2.0 172ms
4 -7.926861196586 -4.57 -3.02 3.0 222ms
5 -7.926861658176 -6.34 -3.48 2.2 187ms
6 -7.926861676245 -7.74 -4.07 1.6 163ms
7 -7.926861677437 -8.92 -4.04 1.9 178ms
8 -7.926861677789 -9.45 -3.99 1.0 151ms
9 -7.926861681707 -8.41 -4.12 1.0 159ms
10 -7.926861681822 -9.94 -4.73 1.0 153ms
11 -7.926861681860 -10.42 -5.27 1.2 164ms
12 -7.926861681865 -11.26 -5.15 1.5 160ms
13 -7.926861681872 -11.21 -5.40 1.0 159ms
14 -7.926861681872 -12.13 -5.50 1.0 158ms
15 -7.926861681872 -12.85 -5.63 1.0 152ms
16 -7.926861681873 -12.85 -6.07 1.0 160ms
17 -7.926861681873 -13.65 -6.42 1.2 156ms
18 -7.926861681873 -14.27 -7.34 1.5 169ms
19 -7.926861681873 -14.35 -7.92 2.6 192ms
20 -7.926861681873 -15.05 -8.08 2.0 188msIf 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 -7.921756349874 -0.69 5.6 240ms
2 -7.926133900348 -2.36 -1.22 1.0 150ms
3 -7.926834239217 -3.15 -2.37 2.0 178ms
4 -7.926861284293 -4.57 -3.01 3.0 214ms
5 -7.926861656314 -6.43 -3.45 2.5 190ms
6 -7.926861674816 -7.73 -4.00 1.5 159ms
7 -7.926861678500 -8.43 -4.09 1.8 174ms
8 -7.926861681345 -8.55 -4.41 1.0 158ms
9 -7.926861681841 -9.30 -4.87 1.2 154ms
10 -7.926861681866 -10.61 -5.56 1.8 173ms
11 -7.926861681872 -11.24 -5.89 2.2 182ms
12 -7.926861681873 -12.11 -6.10 1.4 170ms
13 -7.926861681873 -13.53 -6.32 1.0 151ms
14 -7.926861681873 -13.88 -7.02 1.0 159ms
15 -7.926861681873 + -15.05 -7.07 2.5 190ms
16 -7.926861681873 + -Inf -6.96 1.0 155ms
17 -7.926861681873 -14.75 -8.03 1.0 159msThe 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 -7.921699835210 -0.69 5.5 264ms
2 -7.926137548544 -2.35 -1.22 1.0 136ms
3 -7.926836725738 -3.16 -2.37 2.0 183ms
4 -7.926864709896 -4.55 -2.99 3.0 217ms
5 -7.926865054030 -6.46 -3.37 2.0 160ms
6 -7.926865081022 -7.57 -3.83 1.8 147ms
7 -7.926865090677 -8.02 -4.18 1.5 152msObtaining 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")