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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 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?

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