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")

                       
                       
                       
                       
              Si       
                       
          Si           
                       
                       
                       
                       

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   -7.921684723798                   -0.69    5.6
  2   -7.926167418854       -2.35       -1.22    1.0    215ms
  3   -7.926837141798       -3.17       -2.37    1.8    237ms
  4   -7.926861512551       -4.61       -3.02    2.8    256ms
  5   -7.926861636120       -6.91       -3.36    2.0    250ms
  6   -7.926861666509       -7.52       -3.72    1.8    218ms
  7   -7.926861680518       -7.85       -4.37    1.1    202ms
  8   -7.926861681793       -8.89       -4.89    2.1    233ms
  9   -7.926861681862      -10.16       -5.29    1.8    241ms
 10   -7.926861681872      -11.02       -5.96    2.0    228ms
 11   -7.926861681873      -12.04       -6.77    2.0    234ms
 12   -7.926861681873      -13.39       -7.42    2.4    264ms
 13   -7.926861681873   +  -14.45       -8.22    2.2    234ms

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   -7.921698101427                   -0.69    5.8
  2   -7.926165146536       -2.35       -1.22    1.0    215ms
  3   -7.926837719298       -3.17       -2.37    1.8    238ms
  4   -7.926861518543       -4.62       -3.03    2.8    258ms
  5   -7.926861643788       -6.90       -3.41    1.6    255ms
  6   -7.926861670183       -7.58       -3.81    1.9    222ms
  7   -7.926861680419       -7.99       -4.33    1.6    215ms
  8   -7.926861681776       -8.87       -4.87    1.9    224ms
  9   -7.926861681864      -10.06       -5.35    1.6    245ms
 10   -7.926861681871      -11.11       -5.89    1.6    219ms
 11   -7.926861681873      -11.95       -7.09    1.9    228ms
 12   -7.926861681873      -13.57       -7.61    3.6    300ms
 13   -7.926861681873      -15.05       -8.46    2.0    230ms

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   -7.921691762045                   -0.69    5.9
  2   -7.926170013481       -2.35       -1.22    1.0    203ms
  3   -7.926840264288       -3.17       -2.37    1.9    236ms
  4   -7.926864880882       -4.61       -3.01    2.5    253ms
  5   -7.926865037564       -6.80       -3.33    1.9    222ms
  6   -7.926865076638       -7.41       -3.71    1.5    223ms
  7   -7.926865091700       -7.82       -4.38    1.2    195ms

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")

                       
                       
                       
                       
              Si       
                       
          Si           
                       
                       
                       
                       

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")

                       
                       
                       
                       
              Si       
                       
          Si