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 -7.921744194598 -0.69 5.5 243ms
2 -7.926130951060 -2.36 -1.22 1.0 211ms
3 -7.926833946766 -3.15 -2.37 2.0 165ms
4 -7.926861287800 -4.56 -3.02 2.9 208ms
5 -7.926861660005 -6.43 -3.49 2.2 178ms
6 -7.926861676379 -7.79 -4.09 1.6 156ms
7 -7.926861677912 -8.81 -4.07 2.2 178ms
8 -7.926861678577 -9.18 -4.08 1.0 145ms
9 -7.926861681722 -8.50 -4.14 1.0 152ms
10 -7.926861681843 -9.92 -4.47 1.0 147ms
11 -7.926861681855 -10.95 -4.55 1.0 154ms
12 -7.926861681861 -11.23 -4.68 1.0 144ms
13 -7.926861681871 -11.00 -5.61 1.0 152ms
14 -7.926861681871 -12.11 -5.30 2.0 161ms
15 -7.926861681872 -12.34 -5.25 1.0 153ms
16 -7.926861681872 -12.29 -5.91 1.0 146ms
17 -7.926861681873 -12.90 -6.46 1.0 152ms
18 -7.926861681873 -13.73 -6.56 1.5 157ms
19 -7.926861681873 -13.69 -7.08 1.0 153ms
20 -7.926861681873 + -14.45 -7.49 2.0 173ms
21 -7.926861681873 -14.35 -8.43 1.8 158msIf 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 -7.921730169249 -0.69 5.5 202ms
2 -7.926132037090 -2.36 -1.22 1.0 172ms
3 -7.926833085778 -3.15 -2.37 2.0 164ms
4 -7.926861384047 -4.55 -2.99 2.9 208ms
5 -7.926861649400 -6.58 -3.40 2.0 175ms
6 -7.926861672149 -7.64 -3.90 1.8 157ms
7 -7.926861679705 -8.12 -4.21 1.5 159ms
8 -7.926861681796 -8.68 -5.14 1.5 153ms
9 -7.926861681863 -10.17 -5.25 2.6 195ms
10 -7.926861681869 -11.19 -5.58 1.2 164ms
11 -7.926861681873 -11.46 -6.44 1.1 156ms
12 -7.926861681873 -13.24 -6.88 2.2 170ms
13 -7.926861681873 -14.57 -7.57 1.9 173ms
14 -7.926861681873 -14.45 -7.54 2.1 181ms
15 -7.926861681873 -15.05 -8.86 1.0 148msThe 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 -7.921696873502 -0.69 5.5 253ms
2 -7.926136215682 -2.35 -1.22 1.0 165ms
3 -7.926836637194 -3.15 -2.37 2.0 171ms
4 -7.926864661530 -4.55 -2.99 3.1 233ms
5 -7.926865050567 -6.41 -3.35 1.8 166ms
6 -7.926865078917 -7.55 -3.78 1.2 150ms
7 -7.926865090547 -7.93 -4.18 1.8 156msObtaining 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")