# 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?¶

## How to extend the potential database inside pyiron?¶

## How to link your own executable?¶

## 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 | N_{step} |
simulation time ( fs ) | x | ||

steps | N_{step} |
time steps | x | ||

unwrapped_positions | N_{step} x N_{atom} x 3 |
unwrapped atom coordinates ( Å ) | x | x | x |

positions | N_{step} x N_{atom} x 3 |
wrapped atom coordinates ( Å ) | x | x | x |

velocities | N_{step} x N_{atom} x 3 |
velocity of each atom ( Å/fs ) | |||

forces | N_{step} x N_{atom} x 3 |
force on each atom ( eV/Å ) | x | x | x |

cells | N_{step} x 3 x 3 |
cell dimensions (cf. VASP website) ( Å ) | x | x | x |

energy_tot | N_{step} |
total energy of the system ( eV ) | x | x | x |

energy_kin | N_{step} |
kinetic energy of the system ( eV ) | x | ||

energy_pot | N_{step} |
potential energy of the system ( eV ) | x | ||

pressures | N_{step} x 3 x 3 |
pressures ( GPa ) | x | ||

temperature | N_{step} |
temperature ( K ) | x | x | |

volume | N_{step} ? |
supercell volume ( Å^{3} ) |
x | x | x |

atom_voronoi | N_{step} x N_{atom} |
Voronoi volume of each atom ( Å^{3} ) |
|||

atom_stress | N_{step} x N_{atom} x 3 x 3 |
stress per atom x atomic volume ( eV ) | x | ||

atom_centro | N_{step} x N_{atom} |
centro-symmetry parameter ( Å^{2} ) |
|||

atom_displace | N_{step} x N_{atom} x 3 |
displacement of each atom with respect to the initial position ( Å ) | |||

computation_time | N_{step} |
computation time of the simulation ( s ) | x |

dft | |||||
---|---|---|---|---|---|

tag | dimension | description | VASP | SPHInX | LAMMPS |

(scf_)energy_int | N_{step} |
internal energy ( eV ) | x | ||

(scf_)energy_free | N_{step} |
free energy, same as energy_tot in generic ( eV ) | x | x | |

(scf_)energy_zero | N_{step} |
extrapolated energy, sigma → 0 ( eV ) | x | x | |

(scf_)energy_band | N_{step} |
band gap energy ( eV ) | x | ||

(scf_)residue | N_{step} ( x 2 ) |
energy residue ( eV ) | x | ||

atoms_(scf_)spins | N_{step} x N_{atom} |
spin moment of each atom ( Bohr magneton ) | x | ||

(scf_)magnetic_forces | N_{step} x N_{atom} |
spin forces ? ( eV/Bohr magneton ) | x | ||

atom_spin_constraints | N_{step} x N_{atom} |
spin constraints ( Bohr magneton ) | x | ||

bands_e_fermi | N_{step} |
fermi energy ( eV ) | x | ||

bands_occ | N_{step} ( x 2 ) x N_{k} x N_{states} |
occupancy | x | ||

bands_k_weights | N_{k} |
weight of each k point | x | ||

bands_eigen_values | N_{step} ( x 2 ) x N_{k} x N_{states} |
eigenspectrums ( eV ) | x | ||

scf_convergence | N_{step} |
convergence of each ionic step | x |

- N
_{step}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