simonpintarelli / pysirius-examples

pySIRUS examples

• example-md.py Update atom positions, lattice vectors and update dependent objects (potential, density)
• example-linalg.py Basic linear algebra operations plane-wave coefficients (wfc objects) and occupation numbers
• stiefel_manifold.py Evaluate total energy along a geodesic

Units

Unless otherwise specified, SIRIUS uses Hartree and Bohr. Atom positions are specifed in relative coordinates to the unit cell.

UPF to json conversion

SIRIUS parses pseudopotentials stored as json. A python script to convert from UPF to json is provided by SIRIUS link:

python upf_to_json.py Xe.upf

UPF files can be found in the links below:

• pseudo-dojo
• SSSP
• QuantumESPRESSO

Input file

The following is yaml (json doesn't support comments), however sirius only understands json, use yq . example.yaml to convert to json.

# Schema: https://github.com/electronic-structure/SIRIUS/blob/develop/src/context/input_schema.json
control:
  # processing unit either `cpu` or `gpu`
  processing_unit: cpu
  # verbosity: 0: no output, 1: default output, 2: debug output
  verbosity: 1
parameters:
  # SIRIUS doesn't parse xc funcs from the PP-file, instead `xc_functionals` is used, if empty, no XC contribution is applied
  # for PBE use [XC_GGA_X_PBE, XC_GGA_C_PBE]
  # all available functionals: https://github.com/electronic-structure/SIRIUS/blob/develop/src/potential/xc_functional_base.hpp
  xc_functionals: [XC_LDA_X, XC_LDA_C_PZ]
  # smearing can be `gaussian`, `cold`, `fermi-dirac`
  smearing: gaussian
  # smearing witdh in Hartree
  smearing_width: 0.025
  use_symmetry: true
  # 0:
  num_mag_dims: 0
  # number of bands: -1 -> automatic
  num_fv_states: -1
  # wfc cutoff in Hartree
  gk_cutoff: 6
  # density cutoff in Hartree
  pw_cutoff: 20
  # SCF convergence thresholds
  energy_tol: 1.0e-08
  density_tol: 1.0e-08
  # maximum number of SCF iterations
  num_dft_iter: 100
  # k-point grid
  ngridk: [3, 3, 3]
unit_cell:
  # lattice vectors in Bohr
  lattice_vectors:
    - [5.397057814307557, 0, 0]
    - [2.698528907153779, 4.673989172883661, 0]
    - [2.698528907153779, 2.557996390961221, 4.406679252451386]
  atom_types:
    - Al
    - C
  atom_files:
    Al: Al.json
    C: C.json
  # atom positions in relative coordinates
  atoms:
    Al: [[0, 0, 0], [0.5, 0.5, 0.5]]
    C: [0.25, 0.25, 0.25]
  # optionally atom_coordinate_units can be specified,
  atom_coordinate_units: lattice # use `au` for Bohr, or `A` for Angstroms