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} 
centrosymmetry 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