nanotools.relaxation.general_material module

class nanotools.relaxation.general_material.NBRelaxer(atomcell, relaxation_type='atom_partial_relax', tolerance=0.05, max_steps=100, fix_atoms_index=[0], ase_atoms=None, atoms_relaxed=None)[source]

Bases: object

NBRelaxer class.

The NBRelaxer class is used for the relaxation of atomic structures of general material systems. It uses the pretrained universal neural network potential, CHGNet, to accurately predict atomic forces and energies, facilitating the structural relaxation process using the Atomic Simulation Environment (ASE).

atomcell

The AtomCell object representing the atomic structure.

Type:: AtomCell

relaxation_type

The type of relaxation to perform. Available options are: “atom_partial_relax”: Relax the material while fixing certain atoms.

The indices of the atoms to be fixed are specified using the fix_atoms_index parameter. By default, the first atom is fixed.

“cell_fractional_relax”: Relax the unit cell while keeping the scaled positions fixed. “unconstrained_relax”: Perform a full relaxation without any constraints.

Type:: str

tolerance

The atomic force tolerance for the relaxation. The unit is eV/Å.

Type:: float

max_steps

The maximum number of optimization steps to perform.

Type:: int

fix_atoms_index

The indices of atoms to fix during the relaxation. If not given, by default, the first atom is fixed.

Type:: list

parse_xyz_file(atom_cell)[source]

Parses the AtomCell object to an ASE Atoms object.

Parameters:: atom_cell (AtomCell) – An AtomCell object.
Returns:: An ASE Atoms object. Returns None if atom_cell is None.
Return type:: Atoms
Raises:: ValueError – If atom_cell.pbc is not a list of three booleans.

plot_energy(filename: str | bytes | PathLike | None = None, show=False, trajectory_filename: str = 'relax.traj')[source]

Plot the energy during the optimization and save the plot to a file.

Parameters:

filename (os.Pathlike, optional) – The filename of the file to save the plot to. Defaults to “Energy”.
show (bool, optional) – Whether to display the plot. Defaults to False.
trajectory_filename (str) – The filename of the trajectory file to load.

Raises:

FileNotFoundError – If the trajectory file is not found.

Returns:

None

relax(use_device='cpu')[source]

Perform relaxation based on the relaxation type.

Parameters:: use_device (str, optional) – The device to use for the calculation. Defaults to “cpu”.
Returns:: None

relax_full(calculator)[source]

Perform a full relaxation without any constraints using the provided calculator.

Parameters:: calculator – The calculator to use for the relaxation.
Returns:: None

relax_position(calculator)[source]

Relax the position of atoms using the provided calculator.

Parameters:: calculator – The calculator to use for the relaxation.
Returns:: None

relax_strain(calculator)[source]

Relax the unit cell until the stress is zero while keeping the scaled positions fixed using the provided calculator.

Parameters:: calculator – The calculator to use for the relaxation.
Returns:: None

visualize_trajectory(trajectory_filename: str = 'relax.traj')[source]

Attempts to read a trajectory file and display it.

Parameters:: trajectory_filename (str) – The filename of the trajectory file to load.
Raises:: FileNotFoundError – If the trajectory file is not found, a warning message is printed and the program exits with status code 1.
Returns:: None

write(filename: str | bytes | PathLike | None = None, output_format: str = 'xyz')[source]

Write the relaxed atoms to a file in a specified format.

Parameters:

filename (os.Pathlike, optional) – The filename of the file. Defaults to “relaxed”.
output_format (str, optional) – The format to write the file in. Defaults to “xyz”.

Raises:

ValueError – If self.atoms_relaxed is None or if output_format is not a valid output format.

Returns:

None