parameters

A module for the Parameter and Parameters classes

Parameter defines the name and value of each force field parameter, and whether it is fixed, has constraints or is tied.

Parameters inherits from lists and implements a number of methods for filterting a sequence of Parameter objects.

class MDMC.MD.parameters.Parameter(value, name, fixed=False, constraints=None, **settings)[source]

A force field parameter which can be fixed or constrained within limits

The value of a parameter cannot be set if fixed==True.

Parameters:

value (float) – The value of the parameter.
name (str) – The name of the parameter.
fixed (bool) – Whether or not the value can be changed.
constraints (tuple) – The closed range of the Parameter.value, (lower, upper). constraints must have the same units as value.
**settings –

unit (str)
The unit. If this is not provided then the unit will be taken from the object passed as value.

property interactions: list

Get or append to the parent Interaction objects for this Parameter

Returns:

All parent Interaction objects

Return type:

list

Raises:

ValueError – If an added interaction name is not consistent with existing interaction names
ValueError – If an added Interaction has a function name not consistent with the function names of an existing Interaction

set_tie(parameter: Parameter, expr: str) → None[source]

This ties the Parameter.value to the value of another Parameter

Parameters:

parameter (Parameter) – The Parameter to tie to
expr (str) – A mathematical expression

Examples

To set the Parameter.value to p1.value * 2:

>>> Parameter.set_tie(p1, "* 2")

property tie: float | None

Get the value of a the Parameter that this Parameter is tied to

Returns:: The value of the tied Parameter
Return type:: float

property tied: bool

Get whether this Parameter is tied

Returns:: True if this Parameter is tied to another Parameter, else False
Return type:: bool

static validate_value(value: float, constraints: tuple) → None[source]

Validates the Parameter.value by testing if it is within the constraints

Parameters:

values (float) – The value of the Parameter
constraints (tuple) – A 2-tuple of the lower and upper constraints respectively.

Raises:

ValueError – If the value is not within the constraints

property value: float

Get or set the value of the Parameter

The value will not be changed if it is fixed or tied, or if it is set outside the bounds of constraints

Returns:

The value of the Parameter, including if the Parameter is tied

Return type:

float

Warns:

warnings.warn – If the Parameter is fixed.
warnings.warn – If the Parameter is tied.

class MDMC.MD.parameters.Parameters(init_parameters: Parameter | list[Parameter] | None = None)[source]

A dict-like object where every element is a Parameter indexed by name, which contains a number of helper methods for filtering.

Although Parameters is a dict, it should be treated like a list when writing to it; i.e. initialise it using a list and use append to add to it. These parameters can then be accessed by their name as a key.

In short; Parameters writes like a list and reads like a dict.

Parameters:: init_parameters (Parameter or list of ``Parameter``s, optional, default None) – The initial Parameter objects that the Parameters object contains.

array

An alphabetically-sorted numpy array of the ``Parameter``s stored in this object.

Type:: np.ndarray

append(parameters: list[Parameter] | Parameter) → None[source]

Appends a Parameter or list of ``Parameter``s to the dict, with the parameter name as its key.

Parameters:: parameters (Parameter or list of ``Parameter``s) – The parameter(s) to be added to the dict.

property as_array: ndarray

The parameters in the object as a sorted numpy array.

Returns:: An alphabetically-sorted array of parameter values in the object.
Return type:: np.ndarray

filter(predicate: Callable[[Parameter], bool]) → Parameters[source]

Filters using a predicate

Parameters:: predicate (function) – A function that returns a bool which takes a Parameter as an argument.
Returns:: The Parameter objects which meet the condition of the predicate
Return type:: Parameters

filter_atom_attribute(attribute: str, value: str | float) → Parameters[source]

Filters based on the attribute of Atom objects which have each Parameter applied to them

Parameters:

attribute (str) – An attribute of an Atom. Attributes to match to must be either float or str.
value (str, float) – The value of the Atom attribute.

Returns:

The Parameter objects which are applied to an Atom object which has the specified value of the specified attribute

Return type:

Parameters

filter_function(function_name: str) → Parameters[source]

Filters based on the name of the InteractionFunction of each Parameter

Parameters:: function_name (str) – The name of the InteractionFunction of Parameter objects to return, for example 'LennardJones' or 'HarmonicPotential'.
Returns:: The Parameter objects which have a function with the specified function_name
Return type:: Parameters

filter_interaction(interaction_name: str) → Parameters[source]

Filters based on the name of the Interaction of each Parameter

Parameters:: interaction_name (str) – The name of the Interaction of Parameter objects to return, for example 'Bond'.
Returns:: The Parameter objects which have an Interaction with the specified interaction_name
Return type:: Parameters

filter_name(name: str) → Parameters[source]

Filters by name

Parameters:: name (str) – The name of the Parameter objects to return.
Returns:: The Parameter objects with name
Return type:: Parameters

filter_structure(structure_name: str) → Parameters[source]

Filters based on the name of the Structure to which each Parameter applies

Parameters:: structure_name (str) – The name of a Structure.
Returns:: The Parameter objects which are applied to a Structure which has the specified structure_name
Return type:: Parameters

filter_value(comparison: str, value: float) → Parameters[source]

Filters by value

Parameters:

comparison (str) – A str representing a comparison operator, '>', '<', '>=', '<=', '==', '!='.
value (float) – A float with which Parameter values are compared, using the comparison operator.

Returns:

The Parameter objects which return a True when their values are compared with value using the comparison operator

Return type:

Parameters

log_parameters() → None[source]: Logs all Parameters by ID