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 AtomsBuilder

Feeding 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   -7.921747642553                   -0.69    5.6    216ms
  2   -7.926132235135       -2.36       -1.22    1.0    148ms
  3   -7.926833656834       -3.15       -2.37    2.0    170ms
  4   -7.926861292096       -4.56       -3.01    3.0    276ms
  5   -7.926861653769       -6.44       -3.44    1.9    778ms
  6   -7.926861674177       -7.69       -3.97    1.9    162ms
  7   -7.926861678643       -8.35       -4.10    1.9    161ms
  8   -7.926861681528       -8.54       -4.54    1.1    149ms
  9   -7.926861681844       -9.50       -5.02    1.8    166ms
 10   -7.926861681871      -10.57       -6.01    1.6    184ms
 11   -7.926861681873      -11.72       -5.98    2.8    189ms
 12   -7.926861681873      -13.06       -6.41    1.0    149ms
 13   -7.926861681873      -14.21       -7.18    1.0    152ms
 14   -7.926861681873   +  -14.75       -6.81    2.5    172ms
 15   -7.926861681873      -14.57       -7.80    1.1    157ms
 16   -7.926861681873   +    -Inf       -8.46    2.1    174ms

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   -7.921739306036                   -0.69    5.8    213ms
  2   -7.926131931203       -2.36       -1.22    1.0    196ms
  3   -7.926834245221       -3.15       -2.37    2.1    172ms
  4   -7.926861278991       -4.57       -3.02    2.8    196ms
  5   -7.926861655679       -6.42       -3.46    2.5    179ms
  6   -7.926861675069       -7.71       -4.02    1.5    155ms
  7   -7.926861678551       -8.46       -4.09    2.0    169ms
  8   -7.926861680715       -8.66       -4.29    1.0    150ms
  9   -7.926861681827       -8.95       -4.77    1.2    153ms
 10   -7.926861681863      -10.44       -5.13    1.2    160ms
 11   -7.926861681871      -11.10       -5.49    1.8    162ms
 12   -7.926861681872      -11.74       -6.86    1.2    155ms
 13   -7.926861681873      -12.91       -6.49    3.8    213ms
 14   -7.926861681873      -14.57       -6.63    1.0    152ms
 15   -7.926861681873      -14.75       -7.11    1.0    151ms
 16   -7.926861681873   +  -14.57       -7.50    1.0    150ms
 17   -7.926861681873      -14.75       -8.00    1.0    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   -7.921731793915                   -0.69    5.8    232ms
  2   -7.926135769845       -2.36       -1.22    1.0    140ms
  3   -7.926837637446       -3.15       -2.37    2.0    154ms
  4   -7.926864495273       -4.57       -3.01    3.4    205ms
  5   -7.926865071738       -6.24       -3.43    2.0    159ms
  6   -7.926865086167       -7.84       -3.99    1.5    136ms
  7   -7.926865088907       -8.56       -4.03    1.9    148ms

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")