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 1.116056e+02 1.577682e+00 * time: 1.1378211975097656 1 1.067926e+01 9.056192e-01 * time: 3.4663472175598145 2 -1.131946e+01 9.913793e-01 * time: 4.098193168640137 3 -3.422928e+01 8.071643e-01 * time: 5.055798053741455 4 -4.742222e+01 6.709342e-01 * time: 5.96961522102356 5 -5.682644e+01 2.526858e-01 * time: 6.927574157714844 6 -5.965997e+01 2.395867e-01 * time: 7.567251205444336 7 -6.084517e+01 9.476527e-02 * time: 8.205366134643555 8 -6.139029e+01 4.560247e-02 * time: 8.831188201904297 9 -6.170943e+01 3.827996e-02 * time: 9.455083131790161 10 -6.192500e+01 2.700223e-02 * time: 10.125914096832275 11 -6.204075e+01 2.158195e-02 * time: 10.784012079238892 12 -6.211181e+01 1.774832e-02 * time: 11.405257225036621 13 -6.215154e+01 1.414801e-02 * time: 12.036683082580566 14 -6.217842e+01 9.031055e-03 * time: 12.667927026748657 15 -6.219312e+01 9.374259e-03 * time: 13.337432146072388 16 -6.220125e+01 7.260930e-03 * time: 13.966185092926025 17 -6.220679e+01 6.065130e-03 * time: 14.614784002304077 18 -6.221133e+01 4.860673e-03 * time: 15.235850095748901 19 -6.221484e+01 5.547721e-03 * time: 15.860750198364258 20 -6.221779e+01 6.075807e-03 * time: 16.480419158935547 21 -6.222098e+01 6.794110e-03 * time: 17.095449209213257 22 -6.222482e+01 7.753124e-03 * time: 17.739870071411133 23 -6.222983e+01 7.083213e-03 * time: 18.404795169830322 24 -6.223597e+01 7.483704e-03 * time: 19.03500199317932 25 -6.224298e+01 6.445161e-03 * time: 19.662676095962524 26 -6.224943e+01 5.478181e-03 * time: 20.288406133651733 27 -6.225386e+01 4.142099e-03 * time: 20.92640709877014 28 -6.225680e+01 3.328107e-03 * time: 21.536826133728027 29 -6.225856e+01 3.069448e-03 * time: 22.15044403076172 30 -6.225969e+01 2.049515e-03 * time: 22.78855299949646 31 -6.226045e+01 1.971888e-03 * time: 23.426186084747314 32 -6.226096e+01 1.423891e-03 * time: 24.046499013900757 33 -6.226128e+01 9.983403e-04 * time: 24.702802181243896 34 -6.226146e+01 6.306647e-04 * time: 25.391038179397583 35 -6.226156e+01 5.521364e-04 * time: 26.038703203201294 36 -6.226161e+01 3.488896e-04 * time: 26.68652319908142 37 -6.226163e+01 2.638166e-04 * time: 27.37592911720276 38 -6.226164e+01 2.022540e-04 * time: 28.031264066696167 39 -6.226165e+01 1.685627e-04 * time: 28.688430070877075 40 -6.226166e+01 1.521105e-04 * time: 29.304901123046875 41 -6.226166e+01 1.201817e-04 * time: 29.969714164733887 42 -6.226166e+01 1.018231e-04 * time: 30.629937171936035 43 -6.226166e+01 6.802097e-05 * time: 31.27253818511963 44 -6.226167e+01 5.794624e-05 * time: 31.889150142669678 45 -6.226167e+01 4.031288e-05 * time: 32.5217661857605 46 -6.226167e+01 3.057493e-05 * time: 33.18324899673462 47 -6.226167e+01 2.291599e-05 * time: 33.831873178482056 48 -6.226167e+01 1.981268e-05 * time: 34.49102020263672 49 -6.226167e+01 1.344139e-05 * time: 35.15118718147278 50 -6.226167e+01 1.021034e-05 * time: 35.78208804130554 51 -6.226167e+01 1.031079e-05 * time: 36.43087100982666 52 -6.226167e+01 7.248659e-06 * time: 37.0709011554718 53 -6.226167e+01 6.064941e-06 * time: 37.69280815124512 54 -6.226167e+01 5.772119e-06 * time: 38.350426197052 55 -6.226167e+01 3.954541e-06 * time: 38.98163604736328 56 -6.226167e+01 2.577226e-06 * time: 39.61007809638977 57 -6.226167e+01 2.256983e-06 * time: 40.247496128082275
scfres.energies
Energy breakdown: Kinetic 25.7671066 AtomicLocal -18.8557681 AtomicNonlocal 14.8522652 Ewald -67.1831486 PspCorrection -2.3569765 Hartree 4.8485370 Xc -19.3336820 total -62.261666461969