trajectory

Module for Configuration and related classes

class MDMC.trajectory_analysis.trajectory.AtomCollection[source]

Base class for Configurations

property dimensions: numpy.ndarray

Get the dimensions of the Universe in which the AtomCollection exists

Returns: array – The dimensions of the Universe
Return type: numpy.ndarray

property universe: Optional[Universe]

Get or set the Universe in which the AtomCollection exists

Returns: The Universe in which the AtomCollection exists, or None if it has not been set
Return type: Universe

class MDMC.trajectory_analysis.trajectory.Configuration(*structures: Structure, **settings: dict)[source]

A Configuration stores Atom objects and their positions and velocities

Parameters

*structures – Zero or more Structure objects to be added to the Configuration
**settings –

universe (Universe)
The Universe of the Configuration

element_set

set of the elements in the Configuration

Type: set

universe

Type: Universe or None

data

Type: *structures

add_structure(structures: Structure) → None[source]

Adds the Atom objects from a Structure to the data

Parameters: structures (Structure) – The Structure to add

property atom_positions: list

Get the list of Atom.position which belong to the Configuration

Returns: A list of Atom.position
Return type: list

property atom_velocities: list

Get the list of Atom.velocity which belong to the Configuration

Returns: A list of ``Atom.velocity`
Return type: list

property atoms: list[Atom]

Get the list of Atom which belong to the Configuration

Returns: A list of Atom
Return type: list

property data: numpy.ndarray

Get or set the Atom, Atom.position, and Atom.velocity which belong to the Configuration

Returns: A structured NumPy array with 'atom', 'position', and 'velocity' fields
Return type: numpy.ndarray

property element_list: list

Get the list of Atom.element which belong to the Configuration

Returns: A list of str for the elements
Return type: list

filter_atoms(predicate: function) → list[Atom][source]

Filters the list of Atom using the predicate

Parameters: predicate (function) – A function which returns a bool when passed an Atom
Returns: A list of Atom which are True for the given predicate
Return type: list

filter_by_element(element: str) → list[Atom][source]

Filter the Configuration using an element

Parameters: element (str) – An elemental symbol of the same format as is used for creating Atom objects
Returns: A list of Atom of the specified element
Return type: list

filter_structures(predicate: function) → list[Structure][source]

Filters the list of Structures using the predicate

Parameters: predicate (function) – A function which returns a bool when passed a Structure
Returns: A list of Structures which are True for the given predicate
Return type: list

property molecule_list: list[Molecule]

Get the list of Molecule which belong to the Configuration

Returns: A list of Molecule
Return type: list

scale(factor: float, vectors: str = 'positions') → None[source]

Scales either atom_positions or atom_velocities by a factor

Parameters

factor (float) – Factor by which the vector is scaled
vectors (str, optional) – 'positions' (default) or 'velocities'

Raises

NotImplementedError – THIS IS NOT IMPEMENTED

property structure_list: list[Structure]

Get the list of Structure which belong to the Configuration

Returns: A list of Structure
Return type: list

validate_structure(structure: Structure) → None[source]

Validates the structure by testing that it belongs to the same Universe as the Configuration

Parameters: structure (Structure) – The Structure to validate
Raises: AssertionError – If the Structure does not belong to the same Universe as the Configuration

class MDMC.trajectory_analysis.trajectory.TemporalConfiguration(time: float, *structures: Structure, **settings: dict)[source]

A configuration which has a time associated with it

Parameters

time (float) – The time of the TemporalConfiguration in fs
*structure_units – Zero or more Structures