Creating supercells with pymatgen

The Pymatgen python library allows to setup solid-state calculations using a flexible set of classes as well as an API to an online data base of structures. Its Structure and Lattice objects are directly supported by the DFTK load_atoms and load_lattice functions, such that DFTK may be readily used to run calculation on systems defined in pymatgen. Using the pymatgen_structure function a conversion from DFTK to pymatgen structures is also possible. In the following we use this to create a silicon supercell and find its LDA ground state using direct minimisation.

First we setup the silicon lattice in DFTK.

using DFTK

a = 10.263141334305942  # Lattice constant in Bohr
lattice = a / 2 .* [[0 1 1.]; [1 0 1.]; [1 1 0.]]
Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
atoms = [Si => [ones(3)/8, -ones(3)/8]];

Next we make a [2, 2, 2] supercell using pymatgen

pystruct = pymatgen_structure(lattice, atoms)
pystruct.make_supercell([2, 2, 2])
lattice = load_lattice(pystruct)
atoms = [Si => [s.frac_coords for s in pystruct.sites]];

Setup an LDA model and discretize using a single kpoint and a small Ecut of 5 Hartree.

model = model_LDA(lattice, atoms)
basis = PlaneWaveBasis(model, 5, kgrid=(1, 1, 1))

PlaneWaveBasis (Ecut=5.0, 1 kpoints)

Find the ground state using direct minimisation (always using SCF is boring ...)

scfres = direct_minimization(basis, tol=1e-5);

Iter     Function value   Gradient norm
     0     1.118713e+02     1.470500e+00
 * time: 0.3129560947418213
     1     1.077105e+01     9.259990e-01
 * time: 0.9281599521636963
     2    -1.177957e+01     1.043532e+00
 * time: 1.5687999725341797
     3    -3.439878e+01     7.284206e-01
 * time: 2.4994699954986572
     4    -4.790892e+01     5.797897e-01
 * time: 3.4113359451293945
     5    -5.707470e+01     2.025666e-01
 * time: 4.376496076583862
     6    -5.984404e+01     1.495737e-01
 * time: 4.998073101043701
     7    -6.093995e+01     6.683253e-02
 * time: 5.627810955047607
     8    -6.139529e+01     5.517438e-02
 * time: 6.274214029312134
     9    -6.167571e+01     4.971313e-02
 * time: 6.908367156982422
    10    -6.189403e+01     3.085671e-02
 * time: 7.528775930404663
    11    -6.204903e+01     1.868076e-02
 * time: 8.176185131072998
    12    -6.211311e+01     1.350141e-02
 * time: 8.814064979553223
    13    -6.215621e+01     1.271010e-02
 * time: 9.459475994110107
    14    -6.217906e+01     8.800433e-03
 * time: 10.066012144088745
    15    -6.219260e+01     9.487771e-03
 * time: 10.710416078567505
    16    -6.219996e+01     6.902700e-03
 * time: 11.355996131896973
    17    -6.220525e+01     5.219960e-03
 * time: 11.97954511642456
    18    -6.220976e+01     5.010469e-03
 * time: 12.614872932434082
    19    -6.221304e+01     5.491407e-03
 * time: 13.24311900138855
    20    -6.221628e+01     4.894002e-03
 * time: 13.900515079498291
    21    -6.221947e+01     5.024413e-03
 * time: 14.53973913192749
    22    -6.222319e+01     5.751305e-03
 * time: 15.180062055587769
    23    -6.222798e+01     6.378078e-03
 * time: 15.790297985076904
    24    -6.223382e+01     6.248349e-03
 * time: 16.43066692352295
    25    -6.224008e+01     5.426988e-03
 * time: 17.06340503692627
    26    -6.224654e+01     4.725428e-03
 * time: 17.687673091888428
    27    -6.225173e+01     3.694739e-03
 * time: 18.339781045913696
    28    -6.225531e+01     3.172206e-03
 * time: 18.973438024520874
    29    -6.225766e+01     2.926510e-03
 * time: 19.61459493637085
    30    -6.225917e+01     2.521522e-03
 * time: 20.239139080047607
    31    -6.226018e+01     1.871233e-03
 * time: 20.877249002456665
    32    -6.226081e+01     1.570825e-03
 * time: 21.514836072921753
    33    -6.226119e+01     1.286682e-03
 * time: 22.1438250541687
    34    -6.226142e+01     7.610411e-04
 * time: 22.761234998703003
    35    -6.226154e+01     6.003655e-04
 * time: 23.385180950164795
    36    -6.226160e+01     3.882208e-04
 * time: 24.009618043899536
    37    -6.226163e+01     2.925591e-04
 * time: 24.63848900794983
    38    -6.226164e+01     2.438590e-04
 * time: 25.279049158096313
    39    -6.226165e+01     2.120615e-04
 * time: 25.89560103416443
    40    -6.226166e+01     1.737303e-04
 * time: 26.5398690700531
    41    -6.226166e+01     1.454556e-04
 * time: 27.178143978118896
    42    -6.226166e+01     1.017386e-04
 * time: 27.82778000831604
    43    -6.226166e+01     9.021243e-05
 * time: 28.50462293624878
    44    -6.226166e+01     6.557018e-05
 * time: 29.118685960769653
    45    -6.226167e+01     4.538441e-05
 * time: 29.75104594230652
    46    -6.226167e+01     3.506752e-05
 * time: 30.422138929367065
    47    -6.226167e+01     2.393651e-05
 * time: 31.067146062850952
    48    -6.226167e+01     1.965561e-05
 * time: 31.714259147644043
    49    -6.226167e+01     1.933480e-05
 * time: 32.362168073654175
    50    -6.226167e+01     1.237436e-05
 * time: 33.0032000541687
    51    -6.226167e+01     1.047342e-05
 * time: 33.644843101501465
    52    -6.226167e+01     8.256171e-06
 * time: 34.27035093307495
    53    -6.226167e+01     7.550267e-06
 * time: 34.888867139816284
    54    -6.226167e+01     5.319587e-06
 * time: 35.513832092285156
    55    -6.226167e+01     4.335859e-06
 * time: 36.1313271522522
    56    -6.226167e+01     3.072895e-06
 * time: 36.77915096282959
    57    -6.226167e+01     2.412239e-06
 * time: 37.40871214866638

scfres.energies

Energy breakdown:
    Kinetic             25.7671069
    AtomicLocal         -18.8557644
    AtomicNonlocal      14.8522614
    Ewald               -67.1831486
    PspCorrection       -2.3569765
    Hartree             4.8485367 
    Xc                  -19.3336819

    total               -62.261666461988