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?

Importing existing calculations is currently only supported for VASP. A tutorial how to import existing calculations is available in the tutorial section.

How to import structures from files or existing databases?

To read structure formats you can use ASE and then convert the structure to a pyiron structure using:

from pyiron import ase_to_pyiron
pyiron_structure = ase_to_pyiron(ase_structure)

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 do I install additional codes for pyiron?

When installing pyiron via conda it is possible to install most opensource codes via conda as well:

Install additional codes
code	job_type	How to install ?
GAUSSIAN	Gaussian	Compile on your own (commercial code)
Gpaw	Gpaw	conda install -c conda-forge gpaw
LAMMPS	Lammps	conda install -c conda-forge lammps
S/PHI/nX	Sphinx	conda install -c conda-forge sphinxdft
sqsgenerator	SQSJob	conda install -c conda-forge sqsgenerator
VASP	Vasp	Compile on your own (commercial code)

How to use a custom Pseudo potential in VASP?

There are two ways to assign custom potentials in VASP, either you can change the pseudo potential for all atoms of one species:

job_vasp.potential.Fe = "~/resources/vasp/potentials/potpaw_PBE/Fe/POTCAR"

Or alternatively you can change the pseudo potential of a single atom by creating a new element:

my_fe = pr.create_element(
    new_element_name="Fe",
    parent_element="Fe",
    potential_file="~/resources/vasp/potentials/potpaw_PBE/Fe/POTCAR"
)
job_vasp.structure[0] = my_fe

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

The underlying input of any simulation code in pyiron can be directly accessed. For VASP you can change the INCAR parameters using the VASP specific syntax:

job_vasp.input.incar["ENCUT"] = 320.0  # eV

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?

By default pyiron provides access to the OpenKIM and NIST databases for interatomic potentials and individual potentials can be added as discussed above. While there was an option to extend the default database this option was disabled as it decreased the reproducibility of simulation protocols.

How to link your own executable?

The linking of executables is explained as part of the installation in the section of advanced configuarion options. By default pyiron links to the executables provided by conda but you can accelerate you calculation by compiling your own version of a given simulation code which is optimized for your hardware.

How to send a calculation to the background ?

While most examples execute calculations inline or in modal mode, it is also possible to send calculation in the background.

job.server.run_mode.non_modal = True
job.run()
print("execute other commands while the job is running.")
pr.wait_for_job(job)

In this example the job is executed in the background, while the print command is already executed. Afterwards the project object waits for the execution of the job in the background to be finished.

How to submit a calculation to the queuing system?

Just like executing calculation in the background it is also possible to submit calculation to the queuing system:

job.server.list_queues()  # returns a list of queues available on the system
job.server.view_queues()  # returns a DataFrame listing queues and their settings
job.server.queue = "my_queue"  # select a queue
job.server.cores = 80          # set the number of cores
job.server.run_time = 3600     # set the run time in seconds
job.run()

For the queuing system to be available in pyiron it is necessary to configure it. The configuration of different queuing systems is explained in the installation.

How to setup spin constraint calculation?

pyiron supports setting up spin constrained calculations for VASP using the generic spin_constraint property:

job_vasp.spin_constraints = 1

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 ( Å³ )	x	x	x
atom_voronoi	N_step x N_atom	Voronoi volume of each atom ( Å³ )
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 ( Å² )
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