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 -7.921722336821 -0.69 5.2 194ms
2 -7.926138500384 -2.35 -1.22 1.0 143ms
3 -7.926833450490 -3.16 -2.37 2.0 220ms
4 -7.926861303769 -4.56 -3.01 3.0 205ms
5 -7.926861655258 -6.45 -3.45 2.0 195ms
6 -7.926861674885 -7.71 -4.00 1.9 158ms
7 -7.926861677830 -8.53 -4.05 1.6 157ms
8 -7.926861678283 -9.34 -4.08 1.0 234ms
9 -7.926861681707 -8.47 -4.38 1.0 143ms
10 -7.926861681850 -9.84 -4.67 1.0 936ms
11 -7.926861681843 + -11.17 -4.52 1.1 147ms
12 -7.926861681862 -10.72 -4.77 1.0 146ms
13 -7.926861681869 -11.19 -5.25 1.0 146ms
14 -7.926861681866 + -11.52 -5.01 1.1 149ms
15 -7.926861681872 -11.19 -5.83 1.0 146ms
16 -7.926861681873 -12.80 -6.11 1.2 150ms
17 -7.926861681873 -13.64 -7.13 1.4 152ms
18 -7.926861681873 -14.57 -7.23 3.1 190ms
19 -7.926861681873 + -14.75 -7.75 1.0 155ms
20 -7.926861681873 -14.57 -7.87 1.5 156ms
21 -7.926861681873 + -14.75 -8.31 1.2 150ms
If 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 -7.921715864429 -0.69 5.5 279ms
2 -7.926139424646 -2.35 -1.22 1.0 144ms
3 -7.926834721718 -3.16 -2.37 2.0 166ms
4 -7.926861279054 -4.58 -3.03 2.9 197ms
5 -7.926861659717 -6.42 -3.50 2.1 205ms
6 -7.926861676931 -7.76 -4.11 1.8 160ms
7 -7.926861675138 + -8.75 -3.96 1.8 160ms
8 -7.926861681196 -8.22 -4.42 1.0 151ms
9 -7.926861681810 -9.21 -4.82 1.5 153ms
10 -7.926861681862 -10.28 -5.26 1.5 155ms
11 -7.926861681872 -11.03 -5.98 1.5 162ms
12 -7.926861681873 -12.09 -6.51 2.1 167ms
13 -7.926861681873 -13.03 -6.78 2.0 176ms
14 -7.926861681873 -14.15 -7.05 1.1 154ms
15 -7.926861681873 + -Inf -7.74 1.2 153ms
16 -7.926861681873 -14.57 -7.80 2.4 174ms
17 -7.926861681873 + -14.57 -7.88 1.5 161ms
18 -7.926861681873 -15.05 -8.70 1.0 154ms
The 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 -7.921710163366 -0.69 5.5 212ms
2 -7.926141446582 -2.35 -1.22 1.0 123ms
3 -7.926836719149 -3.16 -2.37 2.0 169ms
4 -7.926864671221 -4.55 -3.00 2.8 183ms
5 -7.926865053160 -6.42 -3.37 2.0 154ms
6 -7.926865080272 -7.57 -3.81 1.5 130ms
7 -7.926865090500 -7.99 -4.17 1.6 138ms
Obtaining 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")