Coordinates

Module containing the different coordinates classes that are used to store and modify positions in space. These can be separated into StandardCoordinates, which is used for ML models, AtomicCoordinates which is used for clusters of atoms, and MolecularCoordinates that stores molecular configurations.

class topsearch.data.coordinates.AtomicCoordinates(atom_labels: list, position: NDArray[Any, Any], bond_cutoff: float = 1.5)

Description

Class to store the coordinates of an atomic system in Euclidean space. Methods to check configurations, modify atomic positions and write configurations to file

bounds

The allowed ranges of the coordinates in each dimension

Type:

list of tuples [(b1_min, b1_max), (b2_min, b2_max)…]

ndim

The dimensionality of the coordinates, 3*n_atoms

Type:

int

position

Array of size ndim containing the current position (x1, y1, z1), …, (x_n, y_n, z_n)

Type:

numpy array

atom_labels

The species in the system, matching the order of position

Type:

list

check_atom_clashes() → bool

Determine if there are atom clashes within the configuration

get_atom(atom_ind: int) → NDArray[Any, Any]

Get the Cartesian position of the atom given index atom_ind

get_connected_atoms() → list

Get the connected atom labels of each atom in cluster

remove_atom_clashes()

Routine to remove clashes between atoms that result in very large gradient values

same_bonds() → bool

Check if we still have a connected network of atoms

write_extended_xyz(energy: float, grad: NDArray[Any, Any], label: str = '') → None

Dump an extended xyz file for visualisation

write_xyz(label: str = '') → None

Dump an xyz file for visualisation

class topsearch.data.coordinates.MolecularCoordinates(atom_labels: list, position: NDArray[Any, Any])

Description

Class to store the coordinates of a molecular system, and methods to modify molecular conformations and write out configurations. Inherits from AtomicCoordinates, but contains additional functionality to generate internal coordinate representation and check bonding structure.

bounds

The allowed ranges of the coordinates in each dimension

Type:

list of tuples [(b1_min, b1_max), (b2_min, b2_max)…]

ndim

The dimensionality of the coordinates, 3*n_atoms

Type:

int

position

Array of size ndim containing the current position

Type:

numpy array

atom_labels

The species in the system, matching the order of position

Type:

list

change_bond_angles(angles: list, step: list, bond_network: Graph) → None

Given a list of bond angles, update them by all by step

change_bond_length(bond: list, length: float, moved_atoms: list) → None

Modify the selected bond length by distance length along the current bond vector

change_bond_lengths(bonds: list, step: list, bond_network: Graph) → None

Given a list of bonds change their bond lengths by step

change_dihedral_angles(bond_dihedrals: list, step: list, bond_network: Graph) → None

Update a list of dihedrals by angles specified in step

get_bond_angle_info() → tuple

Given the current Cartesian coordinates of the atoms in self.position compute all dihedrals, angles and bond lengths needed to define the molecular configuration

get_bonds() → Graph

Find the current bonding framework for self.position

get_connected_atoms() → list

Get the connected atom labels of each atom in molecule

get_movable_atoms(bond: list, bond_type: str, bond_network: Graph) → list

For a given dihedral return the atoms that should be rotated

get_planar_rings() → list

Find the atoms that belong to a planar ring in the molecule

get_repeat_dihedrals(dihedrals: list) → list

Only retain one dihedral when multiple share the same central bond. Returns a list of repeats to remove

get_rotatable_dihedrals() → list

Find all the dihedral angles we can rotate about, along with the atoms that should be rotated for each

get_rotation_matrix(angle: float) → NDArray[Any, Any]

Generate rotation matrix for rotation about x axis

get_specific_bond_angle_info(bonds: list, angles: list, dihedrals: list, permutation: NDArray[Any, Any]) → tuple

Find the bond lengths, bond angles and bond dihedrals for those specified in the input lists, accounting for the permutation of atoms according to permutation

remove_atom_clashes(force_field: type) → None

Check for clashes between atoms. Any atom pairs closer than 0.8*natural_cutoffs can cause a failure for electronic structure calculations so locally minimise to remove clashes with stable empirical force field

remove_repeat_angles(angles: list) → list

To change between conformations we can remove one angle centered on each atom as it is specified by the rest

rotate_angle(angle_atoms: list, angle: float, moved_atoms: list) → None

Rotate one of the bonds in order to change the angle between the two bonds defined by atom0-atom1 and atom1-atom2

rotate_dihedral(bond: list, angle: float, moved_atoms: list) → None

Perform rotation about central bond to change dihedral angle defined between four consecutive atoms

same_bonds() → bool

Compares the bonding framework of the current coordinates with the initial coordinates (self.reference_bonds)

class topsearch.data.coordinates.StandardCoordinates(ndim: int, bounds: list = None)

Description

Class to store a position in space, and the methods to analyse if at bounds

bounds

The allowed ranges of the coordinates in each dimension

Type:

list of tuples [(b1_min, b1_max), (b2_min, b2_max)…]

ndim

The dimensionality of the coordinates

Type:

int

position

Array of size ndim containing the current position

Type:

numpy array

active_bounds() → tuple[NDArray[Any, Any], NDArray[Any, Any]]

Checks whether the position is at the upper or lower bounds

all_bounds() → bool

Check if the position is at the bounds in all dimensions

at_bounds() → bool

Check if the position is at the bounds in any dimension

check_bounds() → NDArray[Any, Any]

Check if position is at the bounds. Returns boolean array denoting which dimensions are at the bounds

generate_random_point() → NDArray[Any, Any]

Return an random point within the bound ranges

move_to_bounds()

Move the coordinates to within the bounds if currently outside