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

Feeding 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    302ms

If 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    379ms

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:
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    288ms

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, 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")