pyiron_atomistics.lammps.lammps.lammps_function

pyiron_atomistics.lammps.lammps.lammps_function(working_directory: str, structure: Atoms, potential: str, calc_mode: str = 'static', calc_kwargs: dict | None = None, cutoff_radius: float | None = None, units: str = 'metal', bonds_kwargs: dict | None = None, server_kwargs: dict | None = None, enable_h5md: bool = False, write_restart_file: bool = False, read_restart_file: bool = False, restart_file: str = 'restart.out', executable_version: str | None = None, executable_path: str | None = None, input_control_file: str | list | dict | None = None)

A single function to execute a LAMMPS calculation based on the LAMMPS job implemented in pyiron

Examples:

>>> import os
>>> from ase.build import bulk
>>> from pyiron_atomistics.lammps.lammps import lammps_function
>>>
>>> shell_output, parsed_output, job_crashed = lammps_function(
...     working_directory=os.path.abspath("lmp_working_directory"),
...     structure=bulk("Al", cubic=True),
...     potential='2009--Mendelev-M-I--Al-Mg--LAMMPS--ipr1',
...     calc_mode="md",
...     calc_kwargs={"temperature": 500.0, "pressure": 0.0, "n_ionic_steps": 1000, "n_print": 100},
...     cutoff_radius=None,
...     units="metal",
...     bonds_kwargs={},
...      enable_h5md=False,
... )

Parameters:

• working_directory (str) – directory in which the LAMMPS calculation is executed

• structure (Atoms) – ase.atoms.Atoms - atomistic structure

• potential (str) – Name of the LAMMPS potential based on the NIST database and the OpenKIM database

• calc_mode (str) – select mode of calculation [“static”, “md”, “minimize”, “vcsgc”]

• calc_kwargs (dict) –

  key-word arguments for the calculate function, the input parameters depend on the calc_mode: “static”: No parameters “md”: “temperature”, “pressure”, “n_ionic_steps”, “time_step”, “n_print”, “temperature_damping_timescale”,

  ”pressure_damping_timescale”, “seed”, “tloop”, “initial_temperature”, “langevin”, “delta_temp”, “delta_press”, job_name”, “rotation_matrix”

  ”minimize”: “ionic_energy_tolerance”, “ionic_force_tolerance”, “max_iter”, “pressure”, “n_print”, “style”,

  ”rotation_matrix”

  ”vcsgc”: “mu”, “ordered_element_list”, “target_concentration”, “kappa”, “mc_step_interval”, “swap_fraction”,

  ”temperature_mc”, “window_size”, “window_moves”, “temperature”, “pressure”, “n_ionic_steps”, “time_step”, “n_print”, “temperature_damping_timescale”, “pressure_damping_timescale”, “seed”, “initial_temperature”, “langevin”, “job_name”, “rotation_matrix”

• cutoff_radius (float) – cut-off radius for the interatomic potential

• units (str) – Units for LAMMPS

• bonds_kwargs (dict) – key-word arguments to create atomistic bonds: “species”, “element_list”, “cutoff_list”, “max_bond_list”, “bond_type_list”, “angle_type_list”,

• server_kwargs (dict) – key-word arguments to create server object - the available parameters are: “user”, “host”, “run_mode”, “queue”, “qid”, “cores”, “threads”, “new_h5”, “structure_id”, “run_time”, “memory_limit”, “accept_crash”, “additional_arguments”, “gpus”, “conda_environment_name”, “conda_environment_path”

• enable_h5md (bool) – activate h5md mode for LAMMPS

• write_restart_file (bool) – enable writing the LAMMPS restart file

• read_restart_file (bool) – enable loading the LAMMPS restart file

• restart_file (str) – file name of the LAMMPS restart file to copy

• executable_version (str) – LAMMPS version to for the execution

• executable_path (str) – path to the LAMMPS executable

• input_control_file (str|list|dict) – Option to modify the LAMMPS input file directly

Returns:

Tuple consisting of the shell output (str), the parsed output (dict) and a boolean flag if

the execution raised an accepted error.

Return type:

str, dict, bool