SimulationUtilities Package

SimulationUtilities.Communication_Codes Module

SimulationUtilities.Communication_Codes.comm_code(label)[source]

This function takes a string describing the type of communication being made and converts it to a machine friendly value.

Parameters:label (str) – The human-readable form of the communication code.
Returns:The machine-readable form of the communication code.
Return type:int

SimulationUtilities.Configuration_Processing Module

SimulationUtilities.Configuration_Processing.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
SimulationUtilities.Configuration_Processing.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
SimulationUtilities.Configuration_Processing.read_configuration_file(configuration_file)[source]

Import the configuration file and store the parsed values in a dictionary.

Parameters:configuration_file (str) – The address of the configuration file as required by the Python open command.
Returns:A dictionary containing the parsed values from the configuration file.
Return type:dict

SimulationUtilities.Curve Module

class SimulationUtilities.Curve.Curve(start_point, end_point, number_of_nodes, total_number_of_nodes)[source]

The purpose of this object is to provide a Curve object that has similar behaviour to that described in [Sutton2013].

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.

total_number_of_nodes

int

The total number of nodes in the curve, including local_nodes - only used to compute the correct scaling of the tangent vector.

tangent

numpy.array

The tangent of the straight line segment joining the start_point to the end_point, rescaled according to [Sutton2013].

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 total movement of the curve as calculated in [Sutton2013].

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.

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_movable_node()[source]

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

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 nodes in default_initial_state are movable.

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.
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.

SimulationUtilities.Extract_States_PDB Module

SimulationUtilities.Extract_States_PDB.extract_states_pdb(pdb_filename, x0_location, xN_location, x0_index, xN_index)[source]

This function is an ASE wrapper that produces a start and end configuration from a PDB file containing multiple conformation.

Parameters:
  • pdb_filename (str) – The location of the PDB file.
  • x0_location (str) – The location of where to write the x0.xyz file, that is the starting configuration.
  • xN_location (str) – The location of where to write the xN.xyz file, the final configuration.
  • x0_index (int) – The index in the PDB file of the starting configuration.
  • xN_index (int) – The index in the PDB file of the final configuration.

SimulationUtilities.Visualize Module

SimulationUtilities.Visualize.write_xyz_animation(curve_pickle, filename)[source]

This function takes a curve object that has been pickled and writes out an XYZ animation file to use with JMol.

Parameters:
  • curve_pickle (str) – The location of a pickled curve object.
  • filename (str) – The location of where to write the XYZ animation.