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     1.114418e+02     1.526206e+00
 * time: 0.047692060470581055
     1     1.049564e+01     8.605299e-01
 * time: 0.14389991760253906
     2    -1.134795e+01     1.060693e+00
 * time: 0.2367839813232422
     3    -3.404157e+01     8.941909e-01
 * time: 0.3957839012145996
     4    -4.740175e+01     6.439889e-01
 * time: 0.5156588554382324
     5    -5.702877e+01     2.358206e-01
 * time: 0.6330578327178955
     6    -5.993787e+01     1.260153e-01
 * time: 0.7251260280609131
     7    -6.101202e+01     5.559138e-02
 * time: 0.8184869289398193
     8    -6.138705e+01     6.000568e-02
 * time: 0.9138128757476807
     9    -6.162523e+01     3.829022e-02
 * time: 1.0091838836669922
    10    -6.181351e+01     2.763832e-02
 * time: 1.1057829856872559
    11    -6.196712e+01     2.065320e-02
 * time: 1.2032098770141602
    12    -6.203423e+01     1.986066e-02
 * time: 1.317816972732544
    13    -6.210270e+01     1.659723e-02
 * time: 1.411789894104004
    14    -6.213859e+01     1.367832e-02
 * time: 1.5082659721374512
    15    -6.217271e+01     1.120699e-02
 * time: 1.6009080410003662
    16    -6.219195e+01     1.026648e-02
 * time: 1.695051908493042
    17    -6.220646e+01     8.779729e-03
 * time: 1.7879760265350342
    18    -6.221666e+01     7.002889e-03
 * time: 1.8813378810882568
    19    -6.222467e+01     7.553672e-03
 * time: 1.974294900894165
    20    -6.223173e+01     6.789086e-03
 * time: 2.0674619674682617
    21    -6.223870e+01     7.977724e-03
 * time: 2.1975958347320557
    22    -6.224586e+01     6.431757e-03
 * time: 2.3457388877868652
    23    -6.225236e+01     5.454031e-03
 * time: 2.452260971069336
    24    -6.225679e+01     3.493221e-03
 * time: 2.5463459491729736
    25    -6.225909e+01     2.430389e-03
 * time: 2.6400208473205566
    26    -6.226021e+01     1.673224e-03
 * time: 2.7346689701080322
    27    -6.226074e+01     1.493230e-03
 * time: 2.8290178775787354
    28    -6.226104e+01     1.197603e-03
 * time: 2.921243906021118
    29    -6.226123e+01     8.886174e-04
 * time: 3.0136139392852783
    30    -6.226137e+01     8.574643e-04
 * time: 3.1082520484924316
    31    -6.226148e+01     6.646317e-04
 * time: 3.2020649909973145
    32    -6.226155e+01     5.598096e-04
 * time: 3.3101859092712402
    33    -6.226160e+01     4.040120e-04
 * time: 3.4022579193115234
    34    -6.226163e+01     2.922187e-04
 * time: 3.4949469566345215
    35    -6.226165e+01     2.480550e-04
 * time: 3.5875749588012695
    36    -6.226166e+01     1.668518e-04
 * time: 3.682229995727539
    37    -6.226166e+01     1.232849e-04
 * time: 3.775825023651123
    38    -6.226166e+01     6.498902e-05
 * time: 3.869248867034912
    39    -6.226166e+01     5.376250e-05
 * time: 3.962890863418579
    40    -6.226167e+01     4.511735e-05
 * time: 4.05699896812439
    41    -6.226167e+01     3.597531e-05
 * time: 4.1641528606414795
    42    -6.226167e+01     2.807706e-05
 * time: 4.258270978927612
    43    -6.226167e+01     2.550638e-05
 * time: 4.352470874786377
    44    -6.226167e+01     2.046943e-05
 * time: 4.445940971374512
    45    -6.226167e+01     1.608685e-05
 * time: 4.538280963897705
    46    -6.226167e+01     1.207549e-05
 * time: 4.630908966064453
    47    -6.226167e+01     8.533072e-06
 * time: 4.724808931350708
    48    -6.226167e+01     7.089667e-06
 * time: 4.818917989730835
    49    -6.226167e+01     5.092450e-06
 * time: 4.914306879043579
    50    -6.226167e+01     3.498343e-06
 * time: 5.008074998855591

scfres.energies

Energy breakdown:
    Kinetic             25.7671069
    AtomicLocal         -18.8557669
    AtomicNonlocal      14.8522634
    Ewald               -67.1831486
    PspCorrection       -2.3569765
    Hartree             4.8485374 
    Xc                  -19.3336822

    total               -62.261666460080