Geometry Module¶

class geometricmd.geometry.Curve(start_point, end_point, number_of_nodes, energy)[source]¶

The purpose of this object is to provide a Curve object with a custom iterator allowing for the Birkhoff algorithm to be applied.

start_point¶

numpy.array

A NumPy array describing the first point in the curve.

end_point¶

numpy.array

A NumPy array describing the last point in the curve.

number_of_nodes¶

int

The total number of nodes that the curve is to consist of, including the start and end points.

energy¶

float

The total Hamiltonian energy to be used in the simulation.

tangent¶

numpy.array

The tangent of the straight line segment joining the start_point to the end_point.

points¶

numpy.array

An NumPy array containing all the points of the curve.

default_initial_state¶

numpy.array

A NumPy array consisting of flags that indicate which nodes are movable initially.

movement¶

float

A variable which records the average movement of nodes in the curve.

nodes_moved¶

numpy.array

A binary NumPy array indicating whether a node has been moved. Used to determine when all the nodes in the curve have been moved.

node_movable¶

numpy.array

A binary NumPy array indicating whether a node is movable.

number_of_distinct_nodes_moved¶

int

A counter recording the total number of nodes that have moved.

configuration¶

dict

A dictionary containing the information from the configuration file.

__init__(start_point, end_point, number_of_nodes, energy)[source]¶

The constructor for the Curve class.

Parameters:	start_point (ase.atoms) – An ASE atoms object describing the initial state. A calculator needs to be set on this object. end_point (ase.atoms) – An ASE atoms object describing the final state. number_of_nodes (int) – The number of nodes that the curve is to consist of, including the start and end points. energy (float) – The total Hamiltonian energy to be used in the simulation.

__iter__()[source]¶

This special method ensures a curve object is iterable.

Returns:	self

all_nodes_moved()[source]¶

This method determines whether every node in the global curve has been tested for length reduction.

Returns:	True if all of the nodes have been tested, False otherwise.
Return type:	bool

get_points()[source]¶

Accessor method for the points attribute.

Returns:	An array containing all of the points of the curve.
Return type:	numpy.array

next()[source]¶

Determine next movable node, given existing information about previously distributed nodes. Used to ensure

the curve object is Python iterable.

Returns:	The node number of the next movable node. If no such node exists then it returns None.
Return type:	int

set_node_movable()[source]¶

Resets all of the flags in the curve to indicate that the current iteration of the Birkhoff algorithm is over.

set_node_position(node_number, new_position)[source]¶

Update the position of the node at node_number to new_position. This processes the logic for releasing neighbouring nodes for further computation.

Parameters:	node_number (int) – The node number of the node whose position is to be updated. new_position (numpy.array) – The new position of the node.

geometricmd.geometry.convert_atoms_to_vector(atoms)[source]¶

Converts an Atomistic Simulation Environment atoms object into a vector which can be used with the curve shortening algorithm.

Parameters:	atoms (ase.atoms) – The ASE atoms object whose position is to be converted to a vector.
Returns:	A vector of atomistic positions.
Return type:	numpy.array

geometricmd.geometry.convert_vector_to_atoms(vector, dimension=3)[source]¶

The inverse of convert_atoms_to_vector.

Parameters:	vector (numpy.array) – The vector containing the position of the atoms to be converted. dimension (optional int) – The dimension of the space in which the simulation is taking place. The default value is 3.
Returns:	An ASE atoms object friendly NumPy array containing the atomistic positions.
Return type:	numpy.array