scine_autocas

Module to provide the Autocas class, which controlls all active space related methods.

Classes

Autocas(molecule[, settings_dict])

Main class to handle all autoCAS functionality.

Exceptions

SingleReferenceException

Raised when autoCAS determines that the system is single reference instead of multireference.

exception scine_autocas.SingleReferenceException

Raised when autoCAS determines that the system is single reference instead of multireference. This allows the client to catch the exception in case they want to perform a single reference calculation afterward.

__doc__ = '\n    Raised when autoCAS determines that the system is single reference\n    instead of multireference. This allows the client to catch the exception\n    in case they want to perform a single reference calculation afterward.\n    '

__module__ = 'scine_autocas'

__weakref__

list of weak references to the object (if defined)

class scine_autocas.Autocas(molecule, settings_dict=None)

Main class to handle all autoCAS functionality.

Attributes

plateau_values	(int, default = 10) determines the minimum length of a plateau
threshold_step	(float, default 0.01) determines the threshold steps in the plateau search and the number of threshold, respectively
cas	(ActiveSpace) stores information on the active space
molecule	(Molecule) stores information about the current molecule
diagnostics	(Diagnostics) stores information from the DMRG calculation
large_spaces	(LargeSpaces) controls settings for the large active space protocol
_excited_states_orbital_indices	(List[int]) stores excited states CAS indices
_excited_states_mod	(int) handles excited states in combination with large cas

__slots__ = ('plateau_values', 'threshold_step', 'cas', 'molecule', 'diagnostics', 'large_spaces', '_excited_states_orbital_indices', '_excited_states_mod')

__init__(molecule, settings_dict=None)

Initialize an autocas object.

The autocas class provides all functionalities to set up active spaces from molecular information, or to apply an active space search based on entopy information from a dmrg calculation.

Parameters

moleculeMolecule

stores molecular information

settings_dictDict[str, Any], optional

holds settings from an autocas yaml input file

plateau_values: int

determines the minimum length of a plateau

threshold_step: float

determines the threshold steps in the plateau search and the number of threshold, respectively

molecule: scine_autocas.autocas_utils.molecule.Molecule

stores information about the current molecule

_excited_states_orbital_indices: List[int]

stores excited states CAS indices

_excited_states_mod: int

handles excited states in combination with large CAS

diagnostics: scine_autocas.autocas_utils.diagnostics.Diagnostics

stores information from the DMRG calculation

large_spaces: scine_autocas.autocas_utils.large_active_spaces.LargeSpaces

controls settings for the large active space protocol

cas: scine_autocas.autocas_utils.active_space.ActiveSpace

stores information on the active space

make_initial_active_space()

Build valence active space.

Returns

cas_occupationsList[int]

a list with int occupations, e.g. 2: doubly occupied, 1: singly occupied, 0: virtual.

cas_indicesList[int]

contains the indices of the orbitals in the active space

rtype

Tuple[List[int], List[int]] ..

__doc__ = '\n    Main class to handle all autoCAS functionality.\n\n    Attributes\n    ----------\n    plateau_values : int, default = 10\n        determines the minimum length of a plateau\n    threshold_step : float, default 0.01\n        determines the threshold steps in the plateau search and the number of threshold, respectively\n    cas : ActiveSpace\n        stores information on the active space\n    molecule : Molecule\n        stores information about the current molecule\n    diagnostics : Diagnostics\n        stores information from the DMRG calculation\n    large_spaces : LargeSpaces\n        controls settings for the large active space protocol\n    _excited_states_orbital_indices : List[int]\n        stores excited states CAS indices\n    _excited_states_mod : int\n        handles excited states in combination with large cas\n    '

__module__ = 'scine_autocas'

_sort_orbitals_by_s1(thresholds_list, orbitals_index)

Sort orbital indices with respect to their threshold value.

Parameters

thresholds_listList[float]

contains the thresholds of s1 values e.g. s1_i / max(s1)

orbitals_indexList[int]

a list with orbitals indices

Returns

thresholds_listList[float]

the ordered tresholds_list

orbitals_indexList[int]

the ordered orbitals_index with respect to the thresholds

rtype

Tuple[ndarray, ndarray] ..

_get_plateau(thresholds_list)

Create a plateau vector from s1 values.

A plateau is complete after not changing the number of orbitals over 10%, e.g. self.plateau_values.

Parameters

thresholds_listnp.ndarray

contains fractions of s1 values, e.g. s1_i / max(s1)

Returns

plateau_vectorList[int]

contains the indices from the plateau

rtype

List[int] ..

_find_plateaus()

Search for a plateau of s1 values.

Returns

plateau_vectorList[int]

the indices from the plateau

orbitals_indexnp.ndarray

indices of the orbitals in the active space

rtype

Tuple[List[int], ndarray] ..

_make_active_space()

Make active space by searching plateaus in s1 and reordering orbitals.

Returns

bool

True if a plateau was found, e.g. a smaller active space; False if no plateau was found

rtype

bool ..

get_active_space(occupation, s1_entropy, s2_entropy=None, mutual_information=None, force_cas=False, xyz_file=None, molecule=None)

Get active space.

autoCAS uses single orbital entropies to decrease the active space size by finding plateaus and including only orbitals with large single orbital entropies

Parameters

occupationList[int]

orbital occupation for each orbital in active space

s1_entropynp.ndarray

single orbital entropy

s2_entropynp.ndarray, optional

two orbital entropy, not required right now

mutual_informationnp.ndarray, optional

mutual information, not required right now

force_cas :: bool

forces to find an active space, even if no orbital has a high single orbital entropy

Returns

cas_occupationsList[int]

the occupation of each orbital in the active space, e.g. 2: doubly occupied, 1: singly occupied, 0: virtual orbital

cas_indicesList[int]

indices of orbitals for the CAS calculation

Raises

AttributeError

if no xyz file was provided

FileNotFoundError

if provided xyz file cannot be found

Exception

if the entropies indicate, that no cas is required, and not forced

NotImplementedError

if a larger cas than valence is theoretically required

rtype

Tuple[List[int], List[int]] ..

_pretty_return()

Ensure that cas occupation is always list of int.

get_large_active_spaces()

Create a list of active spaces for the large active space protocol in autoCAS.

Returns

occupationList[List[int]]

List of occupations for large CAS protocol

orbital_indicesList[List[int]]

List of orbitals indices for large CAS protocol

collect_entropies(indices_list, occupations_list, s1_list, s2_list=None, mut_inf_list=None)

Fill entropy matrices from lists of entropies produced by the large active space protocol.

Parameters

indices_listList[List[int]]

contains several orbital indices from each active space calculation of the large CAS protocol

occupations_listList[List[int]]

contains several orbital occupations for each active space calculation of the large CAS protocol

s1_listList[np.ndarray]

contains several s1 entropies from the large CAS protocol

s2_listList[np.ndarray]

contains several s2 entropies from the large CAS protocol

mut_inf_listList[np.ndarray]

contains several mutual information from the large CAS protocol

Returns

occupationList[int]

the occupation for the large active space

s1_entropynp.ndarray

s1 entropy build and scaled from several entropies

s2_entropynp.ndarray, optional

s2 entropy build and scaled from several entropies

mut_infnp.ndarray, optional

mutual information build and scaled from several mutual information

rtype

Union[Tuple[ndarray, ndarray], Tuple[ndarray, ndarray, ndarray, ndarray]] ..

get_cas_from_large_cas(indices_list, occupations_list, s1_list, s2_list=None, mut_inf_list=None, force_cas=False)

Shortcut function to directly get an active space from the large CAS protocol.

Parameters

indices_listList[List[int]]

contains several orbital indices from each active space calculation of the large CAS protocol

occupations_listList[List[int]]

contains several orbital occupations for each active space calculation of the large CAS protocol

s1_listList[np.ndarray]

contains several s1 entropies from the large CAS protocol

s2_listList[np.ndarray], optional

contains several s2 entropies from the large CAS protocol

mut_inf_listList[np.ndarray], optional

contains several mutual information from the large CAS protocol

force_casbool, optional, default = False

forces to find an active space, even if no orbital has a high single orbital entropy

Returns

cas_occupationsList[int]

the occupation of each orbital in the active space, e.g. 2: doubly occupied, 1: singly occupied, 0: virtual orbital

cas_indicesList[int]

indices of orbitals for the CAS calculation

Raises

ValueError

if something strange happened

rtype

Tuple[List[int], List[int]] ..

get_cas_from_excited_states(occupation, s1_list, s2_list=None, mutual_information_list=None, force_cas=False)

Shortcut function to directly get an active space from excited states.

Parameters

occupationList[int]

contains the orbital occupation for the active space.

s1_listList[np.ndarray]

contains the one orbital entropies for each provided occupation

s2_listList[np.ndarray], optional

contains the two orbital entropies for each provided occupation

mutual_information_listList[np.ndarray], optional

contains the mutual information for each provided occupation

Returns

final_occupationList[int]

contains the occupations of the found active space

final_orbital_indicesList[int]

contains the orbital indices of the found active space

rtype

Tuple[List[int], List[int]] ..

get_cas_from_large_cas_excited_states(indices, occupations, s1_entropy, s2_entropy=None, mut_inf=None, force_cas=False)

Get active space from a large CAS excited state calculation.

Parameters

indices :

contains a list of indices for each state