FAQ

How to cite pyiron?

To cite pyiron and the corresponding codes, please follow the instructions on the publication page.

What units does pyiron use?

  • mass = atomic mass units

  • distance = Angstroms

  • time = femtoseconds

  • energy = eV

  • velocity = Angstroms/femtoseconds

  • force = eV/Angstrom

  • temperature = Kelvin

  • pressure = GPa

  • charge = multiple of electron charge (1.0 is a proton)

How to import existing calculation?

How to import structures from files or existing databases?

How to install pyiron?

pyiron is designed to be installed as centralized service on your local computer cluster, rather than a local installation on each individual workstation. To test pyiron online or with a local installation, please follow the instructions on the installation page.

How to use a custom Pseudo potential in VASP?

How to use VASP tags which are not supported by pyiron?

How to use a custom potential in LAMMPS?

A custom empirical potential (here, a hybrid potential) can be defined in the following format:

custom_potential = pd.DataFrame({
  'Name': ['SrTiO3_Pedone'],
  'Filename': [[]],
  'Model': ['Custom'],
  'Species': [['O', 'Sr', 'Ti']],
  'Config': [['atom_style full\n',  # I use 'full' here as atom_style 'charge' gives the same result
              '## create groups ###\n',
              'group O type 1\n',
              'group Sr type 2\n',
              'group Ti type 3\n',
              '\n',
              '## set charges - beside manually ###\n',
              'set group O charge -1.2000\n',
              'set group Sr charge 1.2000\n',
              'set group Ti charge 2.4000\n',
              '\n',
              'pair_style hybrid/overlay morse 15.0 mie/cut 15.0 coul/long 15.0 beck 15.0\n',
              'pair_coeff * * coul/long\n',
              'pair_coeff 1 2 beck 3.0 0 0 0 0\n',
              'pair_coeff 1 3 beck 1.0 0 0 0 0\n',
              'pair_coeff 1 1 beck 22.0 0 0 0 0\n',
              'pair_coeff 1 2 mie/cut 3.0 1.0 12.0 0\n',
              'pair_coeff 1 3 mie/cut 1.0 1.0 12.0 0\n',
              'pair_coeff 1 1 mie/cut 22.0 1.0 12.0 0\n',
              'pair_coeff 1 2 morse 0.019623 1.8860 3.32833\n',
              'pair_coeff 1 3 morse 0.024235 2.2547 2.708943\n',
              'pair_coeff 1 1 morse 0.042395 1.3793 3.618701\n',
              'kspace_style ewald 1.0e-8\n']]
})

The lines in Config will be written to the LAMMPS potential.inp file. Make sure that the arrangement of the species in Species is the same as the group types create groups within Config. Otherwise, a mixup or the species may occur in the LAMMPS structure.inp file.

The potential can then be used by assigning job.potential = custom_potential.

How to extend the potential database inside pyiron?

How to send a calculation to the background ?

How to submit a calculation to the queuing system?

How to setup spin constraint calculation?

What is the meaning of the name - pyiron?

pyiron is the combination of py + iron connecting Python, the programming language with iron as pyiron was initially developed at the Max Planck Institut für Eisenforschung (iron research).

Which output quantities are stored in pyiron?

generic

tag

dimension

description

VASP

SPHInX

LAMMPS

time

Nstep

simulation time ( fs )

x

steps

Nstep

time steps

x

unwrapped_positions

Nstep x Natom x 3

unwrapped atom coordinates ( Å )

x

x

x

positions

Nstep x Natom x 3

wrapped atom coordinates ( Å )

x

x

x

velocities

Nstep x Natom x 3

velocity of each atom ( Å/fs )

forces

Nstep x Natom x 3

force on each atom ( eV/Å )

x

x

x

cells

Nstep x 3 x 3

cell dimensions (cf. VASP website) ( Å )

x

x

x

energy_tot

Nstep

total energy of the system ( eV )

x

x

x

energy_kin

Nstep

kinetic energy of the system ( eV )

x

energy_pot

Nstep

potential energy of the system ( eV )

x

pressures

Nstep x 3 x 3

pressures ( GPa )

x

temperature

Nstep

temperature ( K )

x

x

volume

Nstep ?

supercell volume ( Å3 )

x

x

x

atom_voronoi

Nstep x Natom

Voronoi volume of each atom ( Å3 )

atom_stress

Nstep x Natom x 3 x 3

stress per atom x atomic volume ( eV )

x

atom_centro

Nstep x Natom

centro-symmetry parameter ( Å2 )

atom_displace

Nstep x Natom x 3

displacement of each atom with respect to the initial position ( Å )

computation_time

Nstep

computation time of the simulation ( s )

x

dft

tag

dimension

description

VASP

SPHInX

LAMMPS

(scf_)energy_int

Nstep

internal energy ( eV )

x

(scf_)energy_free

Nstep

free energy, same as energy_tot in generic ( eV )

x

x

(scf_)energy_zero

Nstep

extrapolated energy, sigma → 0 ( eV )

x

x

(scf_)energy_band

Nstep

band gap energy ( eV )

x

(scf_)residue

Nstep ( x 2 )

energy residue ( eV )

x

atoms_(scf_)spins

Nstep x Natom

spin moment of each atom ( Bohr magneton )

x

(scf_)magnetic_forces

Nstep x Natom

spin forces ? ( eV/Bohr magneton )

x

atom_spin_constraints

Nstep x Natom

spin constraints ( Bohr magneton )

x

bands_e_fermi

Nstep

fermi energy ( eV )

x

bands_occ

Nstep ( x 2 ) x Nk x Nstates

occupancy

x

bands_k_weights

Nk

weight of each k point

x

bands_eigen_values

Nstep ( x 2 ) x Nk x Nstates

eigenspectrums ( eV )

x

scf_convergence

Nstep

convergence of each ionic step

x

  • Nstep refers to ionic steps and not electronic steps

  • properties preceded by scf_ contain the values of each electronic step except for scf_convergence

  • ( x 2 ) refers to the additional column which appears only in magnetic calculations

  • if the crosses under VASP, SPHInX or LAMMPS are missing, the corresponding properties are not implemented