SOAPify.engine

This submodule contains the settings and the function to call the SOAP engines

Module Attributes

KNOWNSOAPENGINES

Literal type for the Known SOAP engine

Functions

`centerMaskCreator`(SOAPatomMask, symbols)	Creates a mask for calculating SOAP only on a subset of the given symbols
`getSoapEngine`(atomNames, SOAPrcut, SOAPnmax, ...)	set up a soap engine with the given settings

Classes

`SOAPengineContainer`(SOAPengine, centerMask, ...)	A container for the SOAP engine
`dscribeSOAPengineContainer`(SOAPengine, ...)	A container for the SOAP engine from dscribe
`quippySOAPengineContainer`(SOAPengine, centerMask)	A container for the SOAP engine from quippy

SOAPify.engine.KNOWNSOAPENGINES

Literal type for the Known SOAP engine

alias of Literal[‘dscribe’, ‘quippy’]

class SOAPify.engine.SOAPengineContainer(SOAPengine, centerMask, SOAPengineKind)[source]

Bases: ABC

A container for the SOAP engine

SOAPengine

the soap engine already set up

Type: SOAP

property SOAPenginekind

retunrs the name of the library used for the engine

Returns: the name of the engine stored
Return type: str

__init__(SOAPengine, centerMask, SOAPengineKind)[source]

property centersMask: Retunr the centersMask

abstract property crossover: bool: returns True if the engine wil calculate the terms for the non same species

property engine

retunrs the sotred engine

Returns: the stored engine
Return type: varies

abstract property features: int: returns the features of the engine

abstract getLocation(specie1, specie2)[source]: returns the slice where the two asked species are stored in the ouput array

abstract property lmax: int: returns the lmax

abstract property nmax: int: returns the nmax

abstract property rcut: int: returns the cutoff radius of the engine

abstract property species: list: returns the species set up fro the engine

SOAPify.engine.centerMaskCreator(SOAPatomMask, symbols)[source]

Creates a mask for calculating SOAP only on a subset of the given symbols

given the list of types of atoms to select and the list od types of atoms in the topology returns the mask of the selected species

the mask is 1 if the atom i is in the SOAPatomMask list, else is 0

Parameters

SOAPatomMask (list[str]) – the mask to apply
symbols (list[str]) – the list of the type of atoms in the trajectory

Returns

the mask of selected atoms

Return type

list[int]

class SOAPify.engine.dscribeSOAPengineContainer(SOAPengine, centerMask)[source]

Bases: SOAPengineContainer

A container for the SOAP engine from dscribe

SOAPengine

the soap engine already set up

Type: SOAP

property SOAPenginekind

retunrs the name of the library used for the engine

Returns: the name of the engine stored
Return type: str

__init__(SOAPengine, centerMask)[source]

property centersMask: Retunr the centersMask

property crossover: bool: returns True if the engine wil calculate the terms for the non same species

property engine

retunrs the sotred engine

Returns: the stored engine
Return type: varies

property features: returns the features of the engine

getLocation(specie1, specie2)[source]: returns the slice where the two asked species are stored in the ouput array

property lmax: returns the lmax

property nmax: returns the nmax

property rcut: returns the cutoff radius of the engine

property species: returns the species set up fro the engine

SOAPify.engine.getSoapEngine(atomNames, SOAPrcut, SOAPnmax, SOAPlmax, SOAPatomMask=None, centersMask=None, SOAP_respectPBC=True, SOAPkwargs=None, useSoapFrom='dscribe')[source]

set up a soap engine with the given settings

please visit the manual of the relative soap engine for the calculation parameters

SOAPatomMask and centersMask are mutually exclusive:

centerMask is a list of atoms whose SOAP fingerprints will be calculate
SOAPatomMask is the list of species that will be included in the centerMask

NB: if you use quippy, we impose it to not normalize the soap vector

Parameters

atomNames (list[str]) – The list of species present in the system
SOAPrcut (float) – the SOAP cut offf
SOAPnmax (int, optional) – The number of radial basis functions (option passed to the desired SOAP engine). Defaults to 8.
SOAPlmax (int, optional) – The maximum degree of spherical harmonics (option passed to the desired SOAP engine). Defaults to 8.
SOAPatomMask (list[str], optional) – the symbols of the atoms whose SOAP fingerprint will be calculated. Defaults to None.
centersMask (Iterable, optional) – the indexes of the atoms whose SOAP fingerprint will be calculated. Defaults to None.
SOAP_respectPBC (bool, optional) –
passed (Determines whether the system is considered to be periodic (option) – to the desired SOAP engine). Defaults to True.
SOAPkwargs (dict, optional) – additional keyword arguments to be passed to the SOAP engine. Defaults to {}.
useSoapFrom (KNOWNSOAPENGINES, optional) – This string determines the selected SOAP engine for the calculations. Defaults to “dscribe”.

Returns

the soap engine set up for the calcualations

Return type

SOAPengineContainer

class SOAPify.engine.quippySOAPengineContainer(SOAPengine, centerMask)[source]

Bases: SOAPengineContainer

A container for the SOAP engine from quippy

SOAPengine

the soap engine already set up

Type: SOAP

property SOAPenginekind

retunrs the name of the library used for the engine

Returns: the name of the engine stored
Return type: str

__init__(SOAPengine, centerMask)[source]

property centersMask: Retunr the centersMask

property crossover: bool: returns True if the engine wil calculate the terms for the non same species

property engine

retunrs the sotred engine

Returns: the stored engine
Return type: varies

property features: returns the features of the engine

getLocation(specie1, specie2)[source]: returns the slice where the two asked species are stored in the ouput array

property lmax: returns the lmax

property nmax: returns the nmax

property rcut: returns the cutoff radius of the engine

property species: returns the species set up fro the engine