Runner

High-level functions for molecular dynamics simulations and structure optimization.

melt_quench_md

melt_quench_md(atoms, calculator: Calculator, *, equi_steps: int = 2500, cool_steps: int = 2500, final_steps: int = 2500, T_high: float = 2000.0, T_low: float = 300.0, time_step: float = 2.0, friction: float = 0.01, trajectory_file: str | None = None, seed: int = 42, verbose: bool = True, log_interval: int = 100)

Run melt-quench molecular dynamics to generate amorphous structures.

Performs a three-stage MD simulation: 1. High-temperature equilibration to melt the structure 2. Controlled cooling to quench the liquid 3. Low-temperature equilibration to relax the structure

Parameters:

Name	Type	Description	Default
atoms	Atoms	ASE Atoms object with initial atomic structure	required
calculator	Calculator	ASE calculator for computing forces and energies	required
equi_steps	int	Number of steps for high-temperature equilibration	2500
cool_steps	int	Number of steps for cooling phase	2500
final_steps	int	Number of steps for final low-temperature equilibration	2500
T_high	float	High temperature for melting phase (K)	2000.0
T_low	float	Low temperature for final phase (K)	300.0
time_step	float	MD time step (fs)	2.0
friction	float	Langevin friction parameter (atomic units)	0.01
trajectory_file	str	Path to save MD trajectory	None
seed	int	Random seed for reproducibility	42
verbose	bool	Whether to print progress information	True
log_interval	int	Number of steps between progress logs	100

Returns:

Name	Type	Description
atoms	Atoms	ASE Atoms with final amorphous structure
log_data	dict	Dictionary with temperature and energy trajectories

relax_unit_cell

relax_unit_cell(atoms: Atoms, calculator: Calculator, *, max_iter: int = 200, fmax: float = 0.01, trajectory_file: str | None = None, verbose: bool = True) -> tuple[Atoms, dict]

Relax atomic positions and cell parameters using FIRE optimization.

Performs simultaneous optimization of atomic positions and unit cell parameters using the Fast Inertial Relaxation Engine (FIRE) algorithm. The cell optimization is handled through ASE's FrechetCellFilter.

Parameters:

Name	Type	Description	Default
atoms	Atoms	ASE Atoms object containing atomic positions, species and cell information	required
calculator	Calculator	ASE calculator for computing energies, forces and stresses	required
max_iter	int	Maximum FIRE iterations, by default 200	200
fmax	float	Force convergence criterion in eV/Å, by default 0.01	0.01
trajectory_file	str	Path to save optimization trajectory, by default None	None
verbose	bool	Print optimization progress, by default True	True

Returns:

Type	Description
tuple[Atoms, dict]	Relaxed Atoms object with optimized positions and cell Dictionary containing energy, forces, stress and volume trajectories

Notes

The calculator must support stress tensor calculations. Periodic boundary conditions must be enabled on the Atoms object.