Base Calculators¶

Calculator
MoleculeCalculator
EAOperation

This module provides calculator classes which serve as abstract base classes for other types for calculators. Note that calculators defined here do not act as direct base classes for calculators which are used by users. The ususal inheritance scheme is Calculator is subclassed by CalculatorType which is subclassed by UserCalculatorType. For example, Calculator is subclassed by Optimizer and Optimizer is subclassed by ETKDG. Only ETKDG is instantiated and used by the user. Note that Optimizer does not subclass Calculator directly, it is subclassed via MolecularCalculator, this is an implementation detail of the Optimizer class.

Calculator simply serves as a common abstract base class for every other stk calculator. The direct subclass of Calculator is an abstract base class which defines a new type of calculator for stk, for example Optimizer or EnergyCalculator. These define an interface for the new type of calculation. Finally the subclasses of Optimizer or EnergyCalculator implement the calculation. For example ETKDG or :class:`.MMFF``or different implementations of an optimization, which the user can use.

For some of the abstract base classes provided here, an implementation is also provided. If the implementation is inherited, the abstract base class it implements should also be inherited, explicitly and directly. This is because inheriting the implementation class is purely an implementation detail that should be treated as invisible to the user of the class.

class Calculator¶

Bases: object

Abstract base class for all calculators.

__init__(self, /, *args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

class EAOperation¶

Bases: stk.calculators.base_calculators.Calculator

Abstract base class for operations such as mutation or crossover.

Methods

set_cache_use(self, use_cache)

Set use of the molecular cache on or off.

__init__(self, /, *args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

set_cache_use(self, use_cache)¶

Set use of the molecular cache on or off.

Parameters: use_cache (bool) – True if the molecular cache is to be used.
Returns: The calculator.
Return type: EAOperation
Raises: NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

class MoleculeCalculator¶

Bases: stk.calculators.base_calculators.Calculator

Abstract base class for calculators used on single molecules.

Methods

`add_to_cache`(self, mol[, value])	Add a molecule to the cache.
`get_cached_value`(self, mol)	Return the value stored in the cache for mol.
`is_caching`(self)	`True` if the calculator has caching turned on.
`is_in_cache`(self, mol)	Return `True` if mol is cached.
`set_cache_use`(self, use_cache)	Set cache use on or off.

__init__(self, /, *args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

add_to_cache(self, mol, value=None)¶

Add a molecule to the cache.

Parameters

mol (Molecule) – The molecule to be added to the cache.
value (class:object, optional) – The cached value associated with the molecule.

Returns

The calculator.

Return type

MoleculeCalculator

Raises

NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

get_cached_value(self, mol)¶

Return the value stored in the cache for mol.

Parameters: mol (Molecule) – The molecule whose cached value is to be returned.
Returns: The cached value.
Return type: object
Raises: NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

is_caching(self)¶

True if the calculator has caching turned on.

Returns: True if the calculator has caching turned on.
Return type: bool
Raises: NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

is_in_cache(self, mol)¶

Return True if mol is cached.

Parameters: mol (Molecule) – The molecule being checked.
Returns: True if mol is cached.
Return type: bool
Raises: NotImplementedError – This is a virtual method and needs to be implemented in a subclass.

set_cache_use(self, use_cache)¶

Set cache use on or off.

Parameters: use_cache (bool) – True if the cache is to be used.
Returns: The calculator.
Return type: MoleculeCalculator
Raises: NotImplementedError – This is a virtual method and needs to be implemented in a subclass.