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 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 ( ns )     x
steps Nstep time steps     x
unwrapped_positions Nstep x Natom x 3 unwrapped atom coordinates ( ) x x x
positions Nstep x Natom x 3 wrapped atom coordinates ( ) x x x
velocities Nstep x Natom x 3 velocity of each atom ( /ns )      
forces Nstep x Natom x 3 force on each atom ( eV/ ) x x x
cells Nstep x 3 x 3 cell dimensions (cf. VASP website) ( ) 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 ( 3 ) x x x
atom_voronoi Nstep x Natom Voronoi volume of each atom ( 3 )      
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 ( 2 )      
atom_displace Nstep x Natom x 3 displacement of each atom with respect to the initial position ( )      
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  
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 )      
bands_occ Nstep occupancy      
bands_k_weights ? ?      
bands_eigen_values Nstep 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
  • if the crosses under VASP, SPHInX or LAMMPS are missing, the corresponding properties are not implemented