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 1.117985e+02 1.590923e+00 * time: 0.3003361225128174 1 1.069771e+01 8.717298e-01 * time: 1.7437100410461426 2 -1.164679e+01 9.936743e-01 * time: 2.2585911750793457 3 -3.385612e+01 7.778561e-01 * time: 3.03285813331604 4 -4.721433e+01 5.949236e-01 * time: 3.790621042251587 5 -5.686587e+01 2.016641e-01 * time: 4.569359064102173 6 -5.976898e+01 1.261770e-01 * time: 5.096089124679565 7 -6.089150e+01 5.426981e-02 * time: 5.603931188583374 8 -6.135051e+01 5.172242e-02 * time: 6.136151075363159 9 -6.161883e+01 3.354035e-02 * time: 6.648972988128662 10 -6.184550e+01 2.645759e-02 * time: 7.163583040237427 11 -6.200032e+01 2.434070e-02 * time: 7.6688551902771 12 -6.207016e+01 2.238588e-02 * time: 8.19186019897461 13 -6.212313e+01 1.573530e-02 * time: 8.715403079986572 14 -6.215300e+01 1.546576e-02 * time: 9.216012001037598 15 -6.217512e+01 1.154445e-02 * time: 9.762562990188599 16 -6.218861e+01 8.847764e-03 * time: 10.271372079849243 17 -6.219859e+01 9.081060e-03 * time: 10.770211219787598 18 -6.220620e+01 6.892419e-03 * time: 11.311005115509033 19 -6.221225e+01 6.860784e-03 * time: 11.860688209533691 20 -6.221770e+01 7.184812e-03 * time: 12.392791032791138 21 -6.222322e+01 7.612277e-03 * time: 12.930358171463013 22 -6.222924e+01 7.607248e-03 * time: 13.456943035125732 23 -6.223590e+01 6.221420e-03 * time: 13.989214181900024 24 -6.224277e+01 4.714710e-03 * time: 14.497457027435303 25 -6.224872e+01 4.793407e-03 * time: 15.014835119247437 26 -6.225334e+01 3.897493e-03 * time: 15.511803150177002 27 -6.225624e+01 3.165638e-03 * time: 16.028808116912842 28 -6.225806e+01 2.641611e-03 * time: 16.52856206893921 29 -6.225930e+01 2.098812e-03 * time: 17.02904200553894 30 -6.226023e+01 1.934131e-03 * time: 17.53640913963318 31 -6.226077e+01 1.799168e-03 * time: 18.046457052230835 32 -6.226113e+01 1.583314e-03 * time: 18.54521417617798 33 -6.226136e+01 1.181721e-03 * time: 19.052999019622803 34 -6.226150e+01 7.151600e-04 * time: 19.556361198425293 35 -6.226159e+01 4.959546e-04 * time: 20.081027030944824 36 -6.226163e+01 2.901746e-04 * time: 20.592272996902466 37 -6.226164e+01 2.625335e-04 * time: 21.09120202064514 38 -6.226165e+01 2.165411e-04 * time: 21.621711015701294 39 -6.226166e+01 1.371886e-04 * time: 22.152387142181396 40 -6.226166e+01 9.780060e-05 * time: 22.660459995269775 41 -6.226166e+01 8.195913e-05 * time: 23.161694049835205 42 -6.226166e+01 5.745397e-05 * time: 23.664014101028442 43 -6.226167e+01 4.921495e-05 * time: 24.173158168792725 44 -6.226167e+01 3.891911e-05 * time: 24.681730031967163 45 -6.226167e+01 3.256673e-05 * time: 25.189527988433838 46 -6.226167e+01 2.447867e-05 * time: 25.687406063079834 47 -6.226167e+01 1.967444e-05 * time: 26.18551206588745 48 -6.226167e+01 1.371401e-05 * time: 26.707045078277588 49 -6.226167e+01 9.160746e-06 * time: 27.2188081741333 50 -6.226167e+01 7.410059e-06 * time: 27.744413137435913 51 -6.226167e+01 5.715342e-06 * time: 28.25138807296753 52 -6.226167e+01 4.625104e-06 * time: 28.7817440032959 53 -6.226167e+01 4.292012e-06 * time: 29.293106079101562 54 -6.226167e+01 3.369651e-06 * time: 29.803954124450684
scfres.energies
Energy breakdown: Kinetic 25.7671077 AtomicLocal -18.8557753 AtomicNonlocal 14.8522699 Ewald -67.1831486 PspCorrection -2.3569765 Hartree 4.8485391 Xc -19.3336827 total -62.261666458357