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 -7.921725789358 -0.69 5.6 246ms
2 -7.926131449480 -2.36 -1.22 1.0 187ms
3 -7.926834208055 -3.15 -2.37 2.0 198ms
4 -7.926861276997 -4.57 -3.02 3.0 207ms
5 -7.926861656008 -6.42 -3.46 1.9 178ms
6 -7.926861674647 -7.73 -4.03 1.9 171ms
7 -7.926861678495 -8.41 -4.09 2.0 168ms
8 -7.926861679121 -9.20 -4.14 1.0 155ms
9 -7.926861681790 -8.57 -4.59 1.0 148ms
10 -7.926861681856 -10.18 -4.74 1.1 158ms
11 -7.926861681863 -11.14 -4.77 1.0 151ms
12 -7.926861681855 + -11.12 -4.91 1.0 161ms
13 -7.926861681865 -11.03 -4.99 1.0 155ms
14 -7.926861681871 -11.18 -5.56 1.0 149ms
15 -7.926861681872 -11.91 -6.22 1.5 162ms
16 -7.926861681872 -13.47 -6.29 1.8 165ms
17 -7.926861681872 -15.05 -6.28 1.0 155ms
18 -7.926861681872 + -14.27 -6.26 1.0 151ms
19 -7.926861681872 -13.75 -6.28 1.0 156ms
20 -7.926861681873 -13.04 -6.62 1.0 154ms
21 -7.926861681873 -13.53 -7.40 1.2 152ms
22 -7.926861681873 + -14.75 -7.67 2.2 181ms
23 -7.926861681873 -15.05 -7.87 1.2 155ms
24 -7.926861681873 + -Inf -8.70 1.4 162msIf 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 -7.921721557105 -0.69 5.6 234ms
2 -7.926127973262 -2.36 -1.22 1.0 174ms
3 -7.926832955564 -3.15 -2.37 2.0 171ms
4 -7.926861320788 -4.55 -2.99 3.0 213ms
5 -7.926861645245 -6.49 -3.39 1.9 179ms
6 -7.926861671030 -7.59 -3.85 1.8 162ms
7 -7.926861679843 -8.05 -4.22 1.2 158ms
8 -7.926861681772 -8.71 -4.97 1.6 162ms
9 -7.926861681858 -10.07 -5.20 2.2 187ms
10 -7.926861681871 -10.89 -5.77 1.4 156ms
11 -7.926861681872 -11.72 -6.34 1.8 179ms
12 -7.926861681873 -12.96 -7.65 1.8 176ms
13 -7.926861681873 -13.97 -7.78 4.0 229ms
14 -7.926861681873 + -Inf -8.48 1.8 170msThe 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 -7.921709114845 -0.69 5.5 280ms
2 -7.926137763092 -2.35 -1.22 1.0 164ms
3 -7.926838208919 -3.15 -2.37 2.0 173ms
4 -7.926864469590 -4.58 -3.02 3.2 232ms
5 -7.926865075784 -6.22 -3.46 1.9 174ms
6 -7.926865087332 -7.94 -4.07 1.6 160msObtaining 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")