pyiron_atomistics.lammps.structure.LammpsStructure

class pyiron_atomistics.lammps.structure.LammpsStructure(bond_dict=None, job=None, atom_type: str = 'atomic')

Bases: LammpsStructure

Parameters:

input_file_name

__init__(bond_dict=None, job=None, atom_type: str = 'atomic')

Methods

__init__([bond_dict, job, atom_type])
get_lammps_id_dict(el_eam_lst)
lammps_header(structure, cell_dimensions, ...)
rotate_positions(structure)	Rotate all atomic positions in given structure according to new Prism cell
rotate_velocities(structure)	Rotate all atomic velocities in given structure according to new Prism cell
simulation_cell()	Returns:
structure_atomic()	Write routine to create atom structure static file that can be loaded by LAMMPS
structure_bond()	Returns:
structure_charge()	Create atom structure including the atom charges.
structure_full()	Write routine to create atom structure static file for atom_type='full' that can be loaded by LAMMPS
write_file(file_name[, cwd])	Write GenericParameters to input file

Attributes

el_eam_lst	Returns:
molecule_ids
potential
structure	Returns:

property el_eam_lst: List[str]

Returns:

rotate_positions(structure: Atoms) → List[Tuple[float, float, float]]

Rotate all atomic positions in given structure according to new Prism cell

Parameters:

structure – Atoms-like object. Should has .positions attribute

Returns:

List of rotated coordinates

Return type:

(list)

rotate_velocities(structure: Atoms) → List[Tuple[float, float, float]]

Rotate all atomic velocities in given structure according to new Prism cell

Parameters:

structure – Atoms-like object. Should have .velocities attribute.

Returns:

List of rotated velocities

Return type:

(list)

simulation_cell() → str

Returns:

property structure

Returns:

structure_atomic() → str

Write routine to create atom structure static file that can be loaded by LAMMPS

Returns:

structure_bond()

Returns:

structure_charge()

Create atom structure including the atom charges.

By convention the LAMMPS atom type numbers are chose alphabetically for the chemical species.

Returns: LAMMPS readable structure.

structure_full()

Write routine to create atom structure static file for atom_type=’full’ that can be loaded by LAMMPS

Returns:

write_file(file_name: str, cwd: str | None = None)

Write GenericParameters to input file

Parameters:

• file_name (str) – name of the file, either absolute (then cwd must be None) or relative

• cwd (str) – path name (default: None)