aiida-eon

AiiDA 2 plugin for eOn. It schedules the eonclient binary. One calculation writes config.ini and the job .con files, runs the client, and parses results.dat.

The Python adaptive kinetic Monte Carlo (AKMC) server is a different process. Use WorkflowFactory("eon.akmc") for independent process searches, or run python -m eon.server for superbasin kinetic Monte Carlo. In-process Matter work is pyeonclient.

The eOn user-guide page is user_guide/aiida.md (TheochemUI/eOn#396).

config.ini is rgpycrumbs.eon.helpers.write_eon_config / eon_schema.config.write_ini. Saddle codes are chemparseplot.parse.eon.saddle_search.EONSaddleStatus. eOn .con geometries convert to Atomic Simulation Environment (ASE) atoms through chemparseplot.parse.eon.con_io.

Install

pip install aiida-eon
verdi plugin list aiida.calculations eon

Register a prebuilt binary:

verdi code create core.code.installed \
  --label eonclient \
  --computer localhost \
  --filepath-executable "$(command -v eonclient)" \
  --default-calc-job-plugin eon

On Elja (login-node AiiDA + Slurm) see docs/elja.md.

Usage

from aiida import orm
from aiida.engine import run
from aiida.plugins import CalculationFactory, DataFactory, WorkflowFactory

EonCalculation = CalculationFactory("eon")
ConData = DataFactory("eon.con")
result = run(
    EonCalculation,
    code=orm.load_code("eonclient@localhost"),
    parameters=orm.Dict(
        dict={
            "Main": {"job": "minimization"},
            "Potential": {"potential": "lj"},
            "Optimizer": {"opt_method": "lbfgs", "converged_force": 0.01},
        }
    ),
    structure=ConData.from_path("pos.con"),
)
print(result["results"].get_dict()["potential_energy"])

Workchains pin the job key and expose the CalcJob ports under calc:

Minimize = WorkflowFactory("eon.minimize")
Neb = WorkflowFactory("eon.neb")
Saddle = WorkflowFactory("eon.saddle")
Process = WorkflowFactory("eon.process_search")
Prefactor = WorkflowFactory("eon.prefactor")
Akmc = WorkflowFactory("eon.akmc")

verdi data eon jobs prints the client catalog. The job key must be a client token (minimization, nudged_elastic_band, oh_tst, and the rest). Aliases such as neb become the magic_enum name before config.ini is written.

Serve mode and forceBatch are not jobs. Potentials (lj, metatomic, rgpot, and the rest) are configuration sections. Copy LAMMPS or Vienna Ab initio Simulation Package (VASP) auxiliaries through the potfiles port.

Tests

pip install -e ".[tests]"
pytest

License

License: Expat (MIT). Contact: rog32@hi.is