Classes#
Models: atomaton.models#
- class atomaton.models.Angle(center_atom, ordered_atoms)#
Bases:
object
- class atomaton.models.Atoms(symbols=array([], dtype=float64), positions=array([], dtype=float64))#
Bases:
objectCollection of Atoms, with methods for calculating bond, angle, dihedral, and improper terms, as well as other important simulation parameters.
Based on (and uses some of) ASE atoms object. Reimplementing is for ease of control, and paedegogical exercise.
- classmethod bind_from_ase(ase_atoms)#
- classmethod bind_from_file(file)#
- calculate_angles()#
- calculate_bonds(cutoffs={'default': [0, 1.5]})#
Finds the bonds between atoms, as defined by the cutoffs dict.
- Args:
cutoffs (dict, optional): Dictionary of bond cutoffs. Keys must match atom types, separated by a -, in alphabetically order. Defaults to {“default”: [0, 1.5]}.
- Returns:
list(list(int, int)): list of bonds, by sorted atom index. list(list[str, str)): list of bond types, sorted alphabetically by atom type. list[list[int, int]]: list of bonds which cross the cell boundary, by sorted orignal atom index. Atoms: list of atoms outside of the cell which are part of bonds crossing the cell. list[list[int, int]]: list of bonds which cross the cell boundary, using the extended atoms index.
- calculate_dihedrals_and_impropers(improper_tol=0.1)#
- center_atom_in_cell()#
- create_extended_cell_minimal(max_bond_length=5.0)#
Creates a minimally extended cell to speed up O(N^2) bond check. This functions is O(N).
- Args:
max_bond_length (float, optional): Maximum possible bond length, used to determine degree to which cell is extended. Defaults to 5.0.
- Raises:
TypeError: max_bond_length must be a single value, or dictionary of bond cutoffs. ValueError: max_bond_length must be less than half the length of the shortes unit cell dimension.
- Returns:
ase.Atoms: minimally extended cell
- get_center_of_positions()#
- shift_atoms(shift)#
- view(**kwargs)#
- class atomaton.models.Improper(center_atom, ordered_atoms)#
Bases:
object