asaplib.descriptors package

Submodules

asaplib.descriptors.atomic_descriptors module

Methods and functions to compute atomic desciptors

class asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_ACSF(desc_spec)

Bases: asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_Base

create(frame)

class asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_Base(desc_spec)

Bases: object

create(frame)

get_acronym()

is_atomic()

class asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_FCHL19(desc_spec)

Bases: asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_Base

Generate the FCHL19 representation (https://doi.org/10.1063/1.5126701). Requires the developer version of the QML package, see https://www.qmlcode.org/installation.html for installation instructions.

:param : :type : param nRs2: Number of gaussian basis functions in the two-body terms :param : :type : type nRs2: integer :param : :type : param nRs3: Number of gaussian basis functions in the three-body radial part :param : :type : type nRs3: integer :param : :type : param nFourier: Order of Fourier expansion :param : :type : type nFourier: integer :param : :type : param eta2: Precision in the gaussian basis functions in the two-body terms :param : :type : type eta2: float :param : :type : param eta3: Precision in the gaussian basis functions in the three-body radial part :param : :type : type eta3: float :param : :type : param zeta: Precision parameter of basis functions in the three-body angular part :param : :type : type zeta: float :param : :type : param two_body_decay: exponential decay for the two body function :param : :type : type two_body_decay: float :param : :type : param three_body_decay: exponential decay for the three body function :param : :type : type three_body_decay: float :param : :type : param three_body_weight: relative weight of the three body function :param : :type : type three_body_weight: float :param : :type : is_periodic: Boolean determining Whether the system is periodic. :param : :type : type Boolean:

create(frame)

class asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_LMBTR(desc_spec)

Bases: asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_Base

create(frame)

class asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_LMBTR_K2(desc_spec)

Bases: asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_LMBTR

class asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_LMBTR_K3(desc_spec)

Bases: asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_LMBTR

class asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_SOAP(desc_spec)

Bases: asaplib.descriptors.atomic_descriptors.Atomic_Descriptor_Base

create(frame)

class asaplib.descriptors.atomic_descriptors.Atomic_Descriptors(desc_spec_dict={})

Bases: object

add(desc_spec, tag)

adding the specifications of a new atomic descriptors :param desc_spec: :type desc_spec: a dictionary that specify which atomic descriptor to use

bind()

binds the objects that actually compute the descriptors these objects need to have .create(frame) method to compute the descriptors of frame (a xyz object)

compute(frame)

compute the global descriptor vector for a frame from atomic contributions :param frame: :type frame: ASE atom object. Coordinates of a frame.

Returns

atomic_desc_dict – and a np.array [N_desc*N_atoms]. Atomic descriptors for a frame. e.g. {‘ad1’:{‘acronym’:’soap-1’, ‘atomic_descriptors’: a np.array [N_desc*N_atoms]}}

Return type

a dictionary. each entry contains the essential info of the descriptor (acronym)

get_acronym()

pack()

asaplib.descriptors.atomic_to_global module

Methods and functions to compute global descriptors of a frame from its atomic desciptors

class asaplib.descriptors.atomic_to_global.Atomic_2_Global_Average(k_spec)

Bases: asaplib.descriptors.atomic_to_global.Atomic_2_Global_Base

this is the vanilla situation. We just take the average soap for all atoms

create(atomic_desc, atomic_numbers=[])

compute the global descriptor vector for a frame from atomic contributions :param atomic_desc: :type atomic_desc: a np.array [N_desc*N_atoms]. Atomic descriptors for a frame. :param atomic_numbers: :type atomic_numbers: np.matrix. [N_atoms]. Atomic numbers for atoms in the frame.

Returns

• acronym (self.acronym)

• desc (a np.array [N_desc]. Global descriptors for a frame.)

class asaplib.descriptors.atomic_to_global.Atomic_2_Global_Base(k_spec)

Bases: object

create(atomic_desc, atomic_numbers=[])

compute the global descriptor vector for a frame from atomic contributions :param atomic_desc: :type atomic_desc: a np.array [N_desc*N_atoms]. Atomic descriptors for a frame. :param atomic_numbers: :type atomic_numbers: np.matrix. [N_atoms]. Atomic numbers for atoms in the frame.

Returns

• acronym (self.acronym)

• desc (a np.array [N_desc]. Global descriptors for a frame.)

get_acronym()

class asaplib.descriptors.atomic_to_global.Atomic_2_Global_Descriptors(k_spec_dict)

Bases: object

add(k_spec, tag)

adding the specifications of a new Atomic_2_Global_Descriptor :param k_spec: :type k_spec: a dictionary that specify which Atomic_2_Global_Descriptor descriptor to use

bind()

binds the objects that actually compute the descriptors these objects need to have .create(atomic_desc) method to compute the global descriptors from atomic ones

compute(atomic_desc_dict, atomic_numbers)

compute the global descriptor vector for a frame from atomic contributions :param atomic_desc_dict: and a np.array [N_desc*N_atoms]. Global descriptors for a frame.

see Atomic_Descriptors.compute() in .atomic_descriptors.py

Parameters

atomic_numbers (np.matrix. [N_atoms] Atomic numbers for atoms in the frame.) –

Returns

desc_dict – and a np.array [N_desc]. Global descriptors for a frame. e.g. {‘d1’:{ ‘acronym’: ‘XXX’, ‘descriptors’: a np.array [N_desc]}}

Return type

a dictionary. each entry contains the essential info of the descriptor, i.e. acronym

pack()

class asaplib.descriptors.atomic_to_global.Atomic_2_Global_Moment_Average(k_spec)

Bases: asaplib.descriptors.atomic_to_global.Atomic_2_Global_Base

get the global descriptor from atomic ones by averaging over the atomic descriptors of z th power

Parameters

zeta (take the zeta th power) –

create(atomic_desc, atomic_numbers=[])

compute the global descriptor vector for a frame from atomic contributions :param atomic_desc: :type atomic_desc: a np.array [N_desc*N_atoms]. Atomic descriptors for a frame. :param atomic_numbers: :type atomic_numbers: np.matrix. [N_atoms]. Atomic numbers for atoms in the frame.

Returns

• acronym (self.acronym)

• desc (a np.array [N_desc]. Global descriptors for a frame.)

class asaplib.descriptors.atomic_to_global.Atomic_2_Global_Moment_Sum(k_spec)

Bases: asaplib.descriptors.atomic_to_global.Atomic_2_Global_Base

get the global descriptor from atomic ones by averaging over the atomic descriptors of z th power

Parameters

zeta (take the zeta th power) –

create(atomic_desc, atomic_numbers=[])

compute the global descriptor vector for a frame from atomic contributions :param atomic_desc: :type atomic_desc: a np.array [N_desc*N_atoms]. Atomic descriptors for a frame. :param atomic_numbers: :type atomic_numbers: np.matrix. [N_atoms]. Atomic numbers for atoms in the frame.

Returns

• acronym (self.acronym)

• desc (a np.array [N_desc]. Global descriptors for a frame.)

class asaplib.descriptors.atomic_to_global.Atomic_2_Global_Sum(k_spec)

Bases: asaplib.descriptors.atomic_to_global.Atomic_2_Global_Base

We just take the sum soap for all atoms

create(atomic_desc, atomic_numbers=[])

compute the global descriptor vector for a frame from atomic contributions :param atomic_desc: :type atomic_desc: a np.array [N_desc*N_atoms]. Atomic descriptors for a frame. :param atomic_numbers: :type atomic_numbers: np.matrix. [N_atoms]. Atomic numbers for atoms in the frame.

Returns

• acronym (self.acronym)

• desc (a np.array [N_desc]. Global descriptors for a frame.)

asaplib.descriptors.atomic_to_global.Descriptor_By_Species(atomic_desc, atomic_numbers, global_species, average_over_natom=True)

first compute the average/sum descriptors for each species, then concatenate them.

Parameters

• atomic_desc (np.matrix. [N_atoms, N_desc] Atomic descriptors for a frame.) –

• atomic_numbers (np.matrix. [N_atoms] Atomic numbers for atoms in the frame.) –

• global_species (a list of all atomic species in all frames) –

• average_over_natom (normalized by number of the atoms of the same species) –

Returns

desc

Return type

np.matrix [N_desc*len(global_species)] Global descriptors for a frame.

asaplib.descriptors.global_descriptors module

Methods and functions to compute global desciptors

class asaplib.descriptors.global_descriptors.Global_Descriptor_Base(desc_spec)

Bases: object

create(frame)

get_acronym()

is_atomic()

class asaplib.descriptors.global_descriptors.Global_Descriptor_CM(desc_spec)

Bases: asaplib.descriptors.global_descriptors.Global_Descriptor_Base

create(frame)

compute the CM descriptor vector for a frame :param frame: :type frame: ASE atom object. Coordinates of a frame.

Returns

• desc_dict (a dictionary. each entry contains the essential info of the descriptor, i.e. acronym) – and a np.array [N_desc]. Global descriptors for a frame. e.g. {‘d1’:{ ‘acronym’: ‘CM-*’, ‘descriptors’: a np.array [N_desc]}}

• atomic_desc_dict ({})

class asaplib.descriptors.global_descriptors.Global_Descriptor_Morgan(desc_spec)

Bases: asaplib.descriptors.global_descriptors.Global_Descriptor_Base

create(frame)

class asaplib.descriptors.global_descriptors.Global_Descriptor_from_Atomic(desc_spec)

Bases: asaplib.descriptors.global_descriptors.Global_Descriptor_Base

create(frame)

compute the global descriptor vector for a frame from atomic contributions :param frame: :type frame: ASE atom object. Coordinates of a frame.

Returns

• desc_dict (a dictionary. each entry contains the essential info of the descriptor, i.e. acronym) – and a np.array [N_desc]. Global descriptors for a frame. e.g. {‘d1’:{ ‘acronym’: ‘XXX’, ‘descriptors’: a np.array [N_desc]}}

• atomic_desc_dict (a dictionary. each entry contains the essential info of the descriptor (acronym)) – and a np.array [N_desc*N_atoms]. Atomic descriptors for a frame. e.g. {‘ad1’:{‘acronym’:’soap-1’, ‘atomic_descriptors’: a np.array [N_desc*N_atoms]}}

pack()

class asaplib.descriptors.global_descriptors.Global_Descriptors(desc_spec_dict={})

Bases: object

add(desc_spec, tag)

adding the specifications of a new atomic descriptors :param desc_spec: :type desc_spec: a dictionary that specify which atomic descriptor to use

bind()

binds the objects that actually compute the descriptors these objects need to have .create(frame) method to compute the descriptors of frame (a xyz object)

compute(frame)

compute the global descriptor vector and atomic descriptor matrix (if any) for a frame :param frame: :type frame: ASE atom object. Coordinates of a frame.

Returns

• desc_dict (a dictionary. each entry contains the essential info of the descriptor, i.e. acronym) – and a np.array [N_desc]. Global descriptors for a frame. e.g. {‘d1’:{ ‘acronym’: ‘XXX’, ‘descriptors’: a np.array [N_desc]}}

• atomic_desc_dict (a dictionary. each entry contains the essential info of the descriptor (acronym)) – and a np.array [N_desc*N_atoms]. Atomic descriptors for a frame. e.g. {‘ad1’:{‘acronym’:’soap-1’, ‘atomic_descriptors’: a np.array [N_desc*N_atoms]}}

pack()

Module contents