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     1.116165e+02     1.595093e+00
 * time: 0.33286309242248535
     1     1.078797e+01     9.156955e-01
 * time: 0.9872231483459473
     2    -1.256763e+01     1.027741e+00
 * time: 1.6302480697631836
     3    -3.463739e+01     8.034406e-01
 * time: 2.5624701976776123
     4    -4.839493e+01     5.524822e-01
 * time: 3.5049710273742676
     5    -5.727998e+01     2.241591e-01
 * time: 4.4793291091918945
     6    -6.004665e+01     1.170688e-01
 * time: 5.133910179138184
     7    -6.108703e+01     4.551192e-02
 * time: 5.7683281898498535
     8    -6.145780e+01     6.834985e-02
 * time: 6.420022010803223
     9    -6.173709e+01     2.848334e-02
 * time: 7.05745005607605
    10    -6.191684e+01     2.481016e-02
 * time: 7.704214096069336
    11    -6.204338e+01     1.747306e-02
 * time: 8.329638004302979
    12    -6.209183e+01     1.318350e-02
 * time: 8.96438717842102
    13    -6.213959e+01     1.253855e-02
 * time: 9.60030221939087
    14    -6.216126e+01     1.178414e-02
 * time: 10.264870166778564
    15    -6.217901e+01     7.905081e-03
 * time: 10.914113998413086
    16    -6.218937e+01     8.512158e-03
 * time: 11.572018146514893
    17    -6.219799e+01     6.994166e-03
 * time: 12.196112155914307
    18    -6.220582e+01     8.828663e-03
 * time: 12.826184034347534
    19    -6.221289e+01     1.069237e-02
 * time: 13.451451063156128
    20    -6.222010e+01     8.963827e-03
 * time: 14.083791017532349
    21    -6.222751e+01     7.772847e-03
 * time: 14.745863199234009
    22    -6.223492e+01     5.076025e-03
 * time: 15.486841201782227
    23    -6.224185e+01     5.212701e-03
 * time: 16.12724804878235
    24    -6.224773e+01     4.344925e-03
 * time: 16.806361198425293
    25    -6.225192e+01     3.753493e-03
 * time: 17.43653702735901
    26    -6.225485e+01     2.844808e-03
 * time: 18.069733142852783
    27    -6.225694e+01     2.704612e-03
 * time: 18.71946120262146
    28    -6.225845e+01     2.781474e-03
 * time: 19.376253128051758
    29    -6.225963e+01     2.216590e-03
 * time: 20.00806713104248
    30    -6.226046e+01     1.803127e-03
 * time: 20.645143032073975
    31    -6.226099e+01     1.130028e-03
 * time: 21.769846200942993
    32    -6.226131e+01     8.939546e-04
 * time: 22.42209506034851
    33    -6.226149e+01     6.091373e-04
 * time: 23.06603217124939
    34    -6.226158e+01     4.862607e-04
 * time: 23.68917417526245
    35    -6.226162e+01     2.906594e-04
 * time: 24.319064140319824
    36    -6.226164e+01     2.455024e-04
 * time: 24.956881999969482
    37    -6.226165e+01     2.291226e-04
 * time: 25.694447994232178
    38    -6.226165e+01     1.646022e-04
 * time: 26.32555913925171
    39    -6.226166e+01     1.312532e-04
 * time: 26.99914813041687
    40    -6.226166e+01     1.165505e-04
 * time: 27.626201152801514
    41    -6.226166e+01     8.940316e-05
 * time: 28.25730800628662
    42    -6.226166e+01     8.340269e-05
 * time: 28.89611315727234
    43    -6.226167e+01     6.053050e-05
 * time: 29.56021213531494
    44    -6.226167e+01     4.171746e-05
 * time: 30.193737030029297
    45    -6.226167e+01     2.133918e-05
 * time: 30.84687614440918
    46    -6.226167e+01     1.495607e-05
 * time: 31.479637145996094
    47    -6.226167e+01     9.295868e-06
 * time: 32.128427028656006
    48    -6.226167e+01     6.786965e-06
 * time: 32.7562141418457
    49    -6.226167e+01     7.795683e-06
 * time: 33.41126203536987
    50    -6.226167e+01     6.297562e-06
 * time: 34.109955072402954
    51    -6.226167e+01     5.727451e-06
 * time: 34.768179178237915
    52    -6.226167e+01     4.335905e-06
 * time: 35.461162090301514
    53    -6.226167e+01     3.264202e-06
 * time: 36.11816906929016
    54    -6.226167e+01     2.526422e-06
 * time: 36.75604605674744
    55    -6.226167e+01     1.679104e-06
 * time: 37.40198016166687
    56    -6.226167e+01     1.260257e-06
 * time: 38.03555417060852

scfres.energies

Energy breakdown:
    Kinetic             25.7671064
    AtomicLocal         -18.8557670
    AtomicNonlocal      14.8522645
    Ewald               -67.1831486
    PspCorrection       -2.3569765
    Hartree             4.8485366 
    Xc                  -19.3336818

    total               -62.261666462800