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 DFTKFeeding an AtomsBase AbstractSystem to DFTK
In this example we construct a silicon system using the ase.build.bulk routine from the atomistic simulation environment (ASE), which is exposed by ASEconvert as an AtomsBase AbstractSystem.
# Construct bulk system and convert to an AbstractSystem
using ASEconvert
system_ase = ase.build.bulk("Si")
system = pyconvert(AbstractSystem, system_ase)FlexibleSystem(Si₂, periodic = TTT):
bounding_box : [ 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")
To use an AbstractSystem in DFTK, we attach pseudopotentials, construct a DFT model, discretise and solve:
system = attach_psp(system; Si="hgh/lda/si-q4")
model = model_LDA(system; 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 -7.921690081665 -0.69 5.8
2 -7.926164785075 -2.35 -1.22 1.0 322ms
3 -7.926837756459 -3.17 -2.37 1.9 360ms
4 -7.926861502049 -4.62 -3.04 2.9 379ms
5 -7.926861648145 -6.84 -3.42 1.8 331ms
6 -7.926861670537 -7.65 -3.82 1.8 324ms
7 -7.926861680304 -8.01 -4.31 1.1 349ms
8 -7.926861681789 -8.83 -4.93 1.9 329ms
9 -7.926861681859 -10.16 -5.23 1.9 354ms
10 -7.926861681871 -10.93 -5.77 1.6 318ms
11 -7.926861681872 -11.72 -6.49 1.9 341ms
12 -7.926861681873 -12.93 -7.75 2.4 361ms
13 -7.926861681873 -14.57 -7.87 4.2 483ms
14 -7.926861681873 + -Inf -8.66 1.0 302msIf we did not want to use ASE we could of course use any other package which yields an AbstractSystem object. This includes:
Reading a system using AtomsIO
using AtomsIO
# Read a file using [AtomsIO](https://github.com/mfherbst/AtomsIO.jl),
# which directly yields an AbstractSystem.
system = load_system("Si.extxyz")
# Now run the LDA calculation:
system = attach_psp(system; Si="hgh/lda/si-q4")
model = model_LDA(system; 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 -7.921673582298 -0.69 6.0
2 -7.926163586549 -2.35 -1.22 1.0 320ms
3 -7.926837637401 -3.17 -2.37 1.9 414ms
4 -7.926861525845 -4.62 -3.05 2.8 377ms
5 -7.926861652801 -6.90 -3.45 1.6 319ms
6 -7.926861673016 -7.69 -3.89 1.8 327ms
7 -7.926861680304 -8.14 -4.29 1.4 317ms
8 -7.926861681730 -8.85 -4.80 1.8 330ms
9 -7.926861681860 -9.88 -5.29 1.8 371ms
10 -7.926861681871 -10.97 -5.80 2.0 347ms
11 -7.926861681873 -11.79 -6.74 1.6 335ms
12 -7.926861681873 -13.17 -8.03 2.5 379msThe 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:
system = attach_psp(system; Si="hgh/lda/si-q4")
model = model_LDA(system; 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 -7.921678080669 -0.69 5.9
2 -7.926166417883 -2.35 -1.22 1.0 305ms
3 -7.926839570192 -3.17 -2.37 1.9 350ms
4 -7.926864884400 -4.60 -2.99 2.4 377ms
5 -7.926865025766 -6.85 -3.29 1.8 307ms
6 -7.926865075581 -7.30 -3.69 1.8 313ms
7 -7.926865091766 -7.79 -4.43 1.4 288msObtaining 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, periodic = TTT):
bounding_box : [ 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, psp=load_psp("hgh/lda/Si-q4"))
atoms = [Si, Si]
positions = [ones(3)/8, -ones(3)/8]
third_system = atomic_system(lattice, atoms, positions)FlexibleSystem(Si₂, periodic = TTT):
bounding_box : [ 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")