Python interface

Jupyter Notebook tutorials illustrating the use of currently available calculations can be found in the janus-tutorials repository. This currently includes examples for:

• Single Point

• Geometry Optimization

• Molecular Dynamics

• Equation of State

• Phonons

Calculation outputs

By default, calculations performed will modify the underlying ase.Atoms object to store information in the Atoms.info and Atoms.arrays dictionaries about the MLIP used.

Additional dictionary keys include arch, corresponding to the MLIP architecture used, and model_path, corresponding to the model path, name or label.

Results from the MLIP calculator, which are typically stored in Atoms.calc.results, will also, by default, be copied to these dictionaries, prefixed by the MLIP arch.

For example:

from janus_core.calculations.single_point import SinglePoint

single_point = SinglePoint(
    struct_path="tests/data/NaCl.cif",
    arch="mace_mp",
    model_path="tests/models/mace_mp_small.model",
)

single_point.run()
print(single_point.struct.info)

will return

{
    'spacegroup': Spacegroup(1, setting=1),
    'unit_cell': 'conventional',
    'occupancy': {'0': {'Na': 1.0}, '1': {'Cl': 1.0}, '2': {'Na': 1.0}, '3': {'Cl': 1.0}, '4': {'Na': 1.0}, '5': {'Cl': 1.0}, '6': {'Na': 1.0}, '7': {'Cl': 1.0}},
    'model_path': 'tests/models/mace_mp_small.model',
    'arch': 'mace_mp',
    'mace_mp_energy': -27.035127799332745,
    'mace_mp_stress': array([-4.78327600e-03, -4.78327600e-03, -4.78327600e-03,  1.08000967e-19, -2.74004242e-19, -2.04504710e-19]),
    'system_name': 'NaCl',
}

Note

If running calculations with multiple MLIPs, arch and mlip_model will be overwritten with the most recent MLIP information. Results labelled by the architecture (e.g. mace_mp_energy) will be saved between MLIPs, unless the same arch is chosen, in which case these values will also be overwritten.

Additional Calculators

Although janus-core only directly supports the MLIP calculators listed in Getting started, any valid ASE calculator can be attached to a structure, including calculators for currently unsupported MLIPs.

This structure can then be passed to janus-core calculations, which can be run as usual.

For example, performing geometry optimisation using the (ASE built-in) Lennard Jones potential calculator:

from janus_core.calculations.geom_opt import GeomOpt
from ase.calculators.lj import LennardJones
from ase.io import read

struct = read("tests/data/NaCl-deformed.cif")
struct.calc = LennardJones()

geom_opt = GeomOpt(
    struct=struct,
    fmax=0.001,
)
geom_opt.run()