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 1.117217e+02 1.554660e+00 * time: 0.33743715286254883 1 1.037440e+01 8.445414e-01 * time: 2.0049779415130615 2 -1.121620e+01 1.050138e+00 * time: 2.6005420684814453 3 -3.365296e+01 7.568869e-01 * time: 3.4959909915924072 4 -4.687883e+01 5.976787e-01 * time: 4.335353136062622 5 -5.666685e+01 2.447570e-01 * time: 5.179017066955566 6 -5.968828e+01 1.751791e-01 * time: 5.786386013031006 7 -6.091866e+01 7.503765e-02 * time: 6.357948064804077 8 -6.140836e+01 4.214580e-02 * time: 6.929265022277832 9 -6.170223e+01 3.050503e-02 * time: 7.494722127914429 10 -6.186184e+01 2.905012e-02 * time: 8.066959142684937 11 -6.195899e+01 2.449689e-02 * time: 8.634283065795898 12 -6.203424e+01 1.852507e-02 * time: 9.224688053131104 13 -6.209407e+01 1.388328e-02 * time: 9.836359024047852 14 -6.213035e+01 1.130053e-02 * time: 10.40229606628418 15 -6.215933e+01 1.133585e-02 * time: 10.9671790599823 16 -6.217571e+01 1.045204e-02 * time: 11.524045944213867 17 -6.218826e+01 6.789764e-03 * time: 12.096714973449707 18 -6.219707e+01 5.088749e-03 * time: 12.673727035522461 19 -6.220342e+01 4.741353e-03 * time: 13.232939958572388 20 -6.220711e+01 3.966608e-03 * time: 13.791857957839966 21 -6.220980e+01 3.217921e-03 * time: 14.341202020645142 22 -6.221183e+01 3.713416e-03 * time: 14.895869970321655 23 -6.221337e+01 3.541477e-03 * time: 15.484123945236206 24 -6.221477e+01 3.923583e-03 * time: 16.072870016098022 25 -6.221642e+01 4.739538e-03 * time: 16.629889965057373 26 -6.221864e+01 4.948514e-03 * time: 17.2029390335083 27 -6.222205e+01 5.584813e-03 * time: 17.772813081741333 28 -6.222672e+01 6.290839e-03 * time: 18.32461714744568 29 -6.223297e+01 6.753165e-03 * time: 18.867797136306763 30 -6.224191e+01 6.664647e-03 * time: 19.42405605316162 31 -6.224791e+01 5.113193e-03 * time: 20.027765035629272 32 -6.225248e+01 4.318983e-03 * time: 20.620769023895264 33 -6.225589e+01 3.248387e-03 * time: 21.202458143234253 34 -6.225830e+01 2.695153e-03 * time: 21.76774311065674 35 -6.225985e+01 1.909121e-03 * time: 22.357434034347534 36 -6.226068e+01 1.449971e-03 * time: 22.9448561668396 37 -6.226108e+01 1.314802e-03 * time: 23.522701025009155 38 -6.226130e+01 1.033844e-03 * time: 24.083203077316284 39 -6.226143e+01 9.213379e-04 * time: 24.65206503868103 40 -6.226152e+01 6.745619e-04 * time: 25.208940982818604 41 -6.226157e+01 4.911401e-04 * time: 25.765687942504883 42 -6.226160e+01 3.851921e-04 * time: 26.34597396850586 43 -6.226163e+01 2.693366e-04 * time: 26.944262981414795 44 -6.226164e+01 3.039109e-04 * time: 27.50420093536377 45 -6.226165e+01 1.799834e-04 * time: 28.06168293952942 46 -6.226166e+01 1.485859e-04 * time: 28.60861301422119 47 -6.226166e+01 1.109399e-04 * time: 29.174752950668335 48 -6.226166e+01 8.379470e-05 * time: 29.727829933166504 49 -6.226166e+01 6.141098e-05 * time: 30.343456983566284 50 -6.226167e+01 4.013468e-05 * time: 30.941395044326782 51 -6.226167e+01 3.271851e-05 * time: 31.5614230632782 52 -6.226167e+01 2.981469e-05 * time: 32.13159894943237 53 -6.226167e+01 2.416664e-05 * time: 32.726853132247925 54 -6.226167e+01 1.946377e-05 * time: 33.33831214904785 55 -6.226167e+01 1.495429e-05 * time: 33.89467906951904 56 -6.226167e+01 1.272462e-05 * time: 34.49176907539368 57 -6.226167e+01 9.765012e-06 * time: 35.09361815452576 58 -6.226167e+01 7.903498e-06 * time: 35.6646511554718 59 -6.226167e+01 5.222971e-06 * time: 36.243205070495605 60 -6.226167e+01 4.097512e-06 * time: 36.815184116363525 61 -6.226167e+01 3.169586e-06 * time: 37.388116121292114 62 -6.226167e+01 2.049678e-06 * time: 37.96784806251526
scfres.energies
Energy breakdown: Kinetic 25.7671066 AtomicLocal -18.8557679 AtomicNonlocal 14.8522650 Ewald -67.1831486 PspCorrection -2.3569765 Hartree 4.8485369 Xc -19.3336819 total -62.261666461562