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. To run this example Julia's PyCall package
needs to be able to find an installation of pymatgen.
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]];
┌ Warning: `vendor()` is deprecated, use `BLAS.get_config()` and inspect the output instead │ caller = npyinitialize() at numpy.jl:67 └ @ PyCall /home/runner/.julia/packages/PyCall/3fwVL/src/numpy.jl:67
Setup an LDA model and discretize using
a single k-point and a small Ecut of 5 Hartree.
model = model_LDA(lattice, atoms)
basis = PlaneWaveBasis(model; Ecut=5, kgrid=(1, 1, 1))
PlaneWaveBasis discretization:
Ecut : 5.0 Ha
fft_size : (32, 32, 32)
kgrid type : Monkhorst-Pack
kgrid : [1, 1, 1]
num. irred. kpoints : 1
Discretized Model(lda_xc_teter93, 3D):
lattice (in Bohr) : [0 , 10.2631 , 10.2631 ]
[10.2631 , 0 , 10.2631 ]
[10.2631 , 10.2631 , 0 ]
unit cell volume : 2162.1 Bohr³
atoms : Si₁₆
atom potentials : ElementPsp(Si, psp=hgh/lda/si-q4)
num. electrons : 64
spin polarization : none
temperature : 0 Ha
terms : Kinetic(1)
AtomicLocal()
AtomicNonlocal()
Ewald()
PspCorrection()
Hartree(1)
Xc([:lda_xc_teter93], 1, nothing)
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 1.127665e+02 1.606264e+00
* time: 0.6813020706176758
1 1.102113e+01 9.131531e-01
* time: 1.9149129390716553
2 -1.220498e+01 1.003073e+00
* time: 2.5312600135803223
3 -3.431502e+01 7.718194e-01
* time: 3.4145729541778564
4 -4.808367e+01 5.306985e-01
* time: 4.330345153808594
5 -5.708626e+01 1.905927e-01
* time: 5.2445759773254395
6 -5.987112e+01 1.060438e-01
* time: 5.848098993301392
7 -6.090861e+01 5.019898e-02
* time: 6.447036027908325
8 -6.129330e+01 5.690215e-02
* time: 7.047147035598755
9 -6.159423e+01 3.711250e-02
* time: 7.6310529708862305
10 -6.180460e+01 2.781044e-02
* time: 8.25081992149353
11 -6.196505e+01 1.742607e-02
* time: 8.833728075027466
12 -6.202623e+01 1.612862e-02
* time: 9.419173955917358
13 -6.208966e+01 1.361778e-02
* time: 10.022592067718506
14 -6.212275e+01 1.399923e-02
* time: 10.64862608909607
15 -6.215683e+01 1.274281e-02
* time: 11.240405082702637
16 -6.218055e+01 1.113331e-02
* time: 11.818444013595581
17 -6.219644e+01 7.867465e-03
* time: 12.443083047866821
18 -6.220863e+01 6.479617e-03
* time: 13.03515911102295
19 -6.221581e+01 7.018942e-03
* time: 13.640233993530273
20 -6.222156e+01 8.555744e-03
* time: 14.274359941482544
21 -6.222693e+01 8.129904e-03
* time: 14.878632068634033
22 -6.223305e+01 6.875692e-03
* time: 15.519186019897461
23 -6.223939e+01 6.258161e-03
* time: 16.127515077590942
24 -6.224536e+01 5.625647e-03
* time: 16.754805088043213
25 -6.225068e+01 4.487478e-03
* time: 17.370190143585205
26 -6.225468e+01 3.762597e-03
* time: 17.985623121261597
27 -6.225731e+01 2.608814e-03
* time: 18.609884023666382
28 -6.225884e+01 2.552003e-03
* time: 19.22965097427368
29 -6.225982e+01 1.754205e-03
* time: 19.824806928634644
30 -6.226047e+01 1.777548e-03
* time: 20.458758115768433
31 -6.226090e+01 1.375625e-03
* time: 21.07746696472168
32 -6.226118e+01 1.029226e-03
* time: 21.656898975372314
33 -6.226139e+01 8.291170e-04
* time: 22.243086099624634
34 -6.226152e+01 5.685170e-04
* time: 22.854833126068115
35 -6.226159e+01 4.788458e-04
* time: 23.467275142669678
36 -6.226163e+01 3.158293e-04
* time: 24.047385931015015
37 -6.226165e+01 2.020799e-04
* time: 24.682228088378906
38 -6.226166e+01 1.715368e-04
* time: 25.28341794013977
39 -6.226166e+01 1.022627e-04
* time: 25.914152145385742
40 -6.226166e+01 8.447038e-05
* time: 26.54927897453308
41 -6.226166e+01 7.183904e-05
* time: 27.177632093429565
42 -6.226166e+01 6.062900e-05
* time: 27.8263840675354
43 -6.226167e+01 4.902286e-05
* time: 28.424849033355713
44 -6.226167e+01 3.748563e-05
* time: 29.03422999382019
45 -6.226167e+01 3.233952e-05
* time: 29.61795997619629
46 -6.226167e+01 2.514306e-05
* time: 30.203439950942993
47 -6.226167e+01 1.679244e-05
* time: 30.83185911178589
48 -6.226167e+01 1.195956e-05
* time: 31.44237995147705
49 -6.226167e+01 1.100932e-05
* time: 32.03841805458069
50 -6.226167e+01 6.349492e-06
* time: 32.65385413169861
51 -6.226167e+01 4.615798e-06
* time: 33.2709641456604
52 -6.226167e+01 4.007953e-06
* time: 33.85377311706543
53 -6.226167e+01 3.444816e-06
* time: 34.46028804779053
scfres.energies
Energy breakdown (in Ha):
Kinetic 25.7671068
AtomicLocal -18.8557675
AtomicNonlocal 14.8522645
Ewald -67.1831486
PspCorrection -2.3569765
Hartree 4.8485369
Xc -19.3336819
total -62.261666457831