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 -7.921702254362 -0.69 5.5 189ms
2 -7.926139205052 -2.35 -1.22 1.0 139ms
3 -7.926835292286 -3.16 -2.37 2.0 212ms
4 -7.926861271557 -4.59 -3.03 2.9 191ms
5 -7.926861660793 -6.41 -3.49 2.1 188ms
6 -7.926861676421 -7.81 -4.10 1.5 148ms
7 -7.926861676634 -9.67 -4.01 2.2 163ms
8 -7.926861680666 -8.39 -4.28 1.0 146ms
9 -7.926861681805 -8.94 -4.64 1.1 142ms
10 -7.926861681867 -10.21 -5.04 1.0 147ms
11 -7.926861681870 -11.54 -5.49 1.4 154ms
12 -7.926861681872 -11.58 -6.09 2.0 161ms
13 -7.926861681873 -12.86 -6.34 1.9 168ms
14 -7.926861681873 -13.67 -6.95 1.0 146ms
15 -7.926861681873 -14.75 -7.19 1.9 169ms
16 -7.926861681873 -14.57 -8.47 1.1 143ms
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 -7.921704534646 -0.69 5.4 280ms
2 -7.926139609384 -2.35 -1.22 1.0 140ms
3 -7.926834158305 -3.16 -2.37 2.0 208ms
4 -7.926861279339 -4.57 -3.02 2.9 198ms
5 -7.926861655684 -6.42 -3.46 2.1 162ms
6 -7.926861674983 -7.71 -4.02 1.6 158ms
7 -7.926861677437 -8.61 -4.04 2.0 170ms
8 -7.926861676306 + -8.95 -3.99 1.0 147ms
9 -7.926861681555 -8.28 -4.29 1.0 140ms
10 -7.926861681731 -9.75 -4.25 1.0 146ms
11 -7.926861681815 -10.07 -4.31 1.0 148ms
12 -7.926861681850 -10.46 -4.45 1.0 149ms
13 -7.926861681854 -11.39 -4.47 1.0 142ms
14 -7.926861681839 + -10.82 -4.31 1.0 249ms
15 -7.926861681860 -10.67 -4.57 1.0 1.07s
16 -7.926861681872 -10.93 -5.26 1.0 141ms
17 -7.926861681870 + -11.70 -4.86 1.0 141ms
18 -7.926861681873 -11.59 -6.89 1.0 141ms
19 -7.926861681873 -13.24 -7.19 2.9 187ms
20 -7.926861681873 -14.57 -7.27 1.1 144ms
21 -7.926861681873 + -Inf -7.57 1.0 141ms
22 -7.926861681873 + -15.05 -7.50 1.0 141ms
23 -7.926861681873 -14.45 -7.71 1.0 140ms
24 -7.926861681873 + -14.57 -8.25 1.5 150ms
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 -7.921711872529 -0.69 5.5 206ms
2 -7.926139630130 -2.35 -1.22 1.0 119ms
3 -7.926837182922 -3.16 -2.37 2.0 172ms
4 -7.926864708483 -4.56 -3.02 3.1 189ms
5 -7.926865066675 -6.45 -3.47 2.1 145ms
6 -7.926865086097 -7.71 -4.05 1.6 132ms
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")