`esipy`¶

Submodules¶

Package Contents¶

Classes¶

`IndicatorsRest`
`IndicatorsUnrest`	Initialize the indicators from Unrestricted calculations.
`IndicatorsNatorb`	Initialize the indicators from Natural Orbitals calculations.
`ESI`	Main class for the ESIpy code.

Functions¶

`write_aoms`(mol, mf, name, aom[, ring, partition])	Writes the input for the ESI-3D code from the AOMs.
`read_aoms`([path])	Reads the AOMs from ESIpy's writeaoms() method or from an AIMAll calculation.
`read_molinfo`(path)	Reads all *.int files from a directory and builds the molinfo dictionary.
`compute_iring`(arr, aom)	Calculation of the Iring aromaticity index.
`sequential_mci`(arr, aom, partition)	Computes the MCI sequentially by computing the Iring without storing the permutations.
`multiprocessing_mci`(arr, aom, ncores, partition)	Computes the MCI by generating all the permutations for a later distribution along the specified number of cores.
`compute_av1245`(arr, aom, partition)	Computes the AV1245 and AVmin indices. Not available for rings smaller than 6 members.
`compute_pdi`(arr, aom)	Computes the PDI for the given 6-membered ring connectivity. Only computed for rings n=6.
`compute_flu`(arr, molinfo, aom[, flurefs, partition])	Computes the FLU index.
`compute_boa`(arr, aom)	Computes the BOA and BOA_c indices.
`compute_homer`(arr, molinfo[, homerrefs])	Computes the HOMER index.
`compute_homa`(arr, molinfo[, homarefs])	Computes the HOMA index.
`compute_bla`(arr, molinfo)	Computes the BLA and BLA_c indices.
`compute_iring_no`(arr, aom)	Calculation of the Iring aromaticity index for correlated wavefunctions.
`sequential_mci_no`(arr, aom, partition)	Computes the MCI for correlated wavefunctions sequentially by computing the Iring without storing the permutations.
`multiprocessing_mci_no`(arr, aom, ncores, partition)	Computes the MCI for correlated wavefunctions by generating all the permutations for a later distribution along the specified number of cores.
`compute_av1245_no`(arr, aom, partition)	Computes the AV1245 and AVmin indices for correlated wavefunctions. Not available for rings smaller than 6 members.
`compute_pdi_no`(arr, aom)	Computes the PDI for the given 6-membered ring connectivity. Only computed for rings n=6.
`compute_boa_no`(arr, aom)	Computes the BOA and BOA_c indices for correlated wavefunctions.
`make_aoms`
`mol_info`([mol, mf, save, partition, connec])	Obtains information from the molecule and the calculation to complement the main code function without requiring the 'mol' and 'mf' objects.
`format_partition`(partition)
`load_file`(file)	Loads a variable from a file.
`format_short_partition`(partition)
`wf_type`(aom)	Checks the topology of the AOMs to obtain the type of wavefunction.
`save_file`(file, save)	Saves a variable to a file.
`build_connec_rest`(Smo[, thres])
`build_connec_unrest`(Smo[, thres])
`build_connec_no`(Smo[, thres])
`find_rings`(connec[, minlen, maxlen, exclude])
`process_fragments`(aom, rings[, done])	Processes fragments by combining AOMs and updating rings.
`build_connectivity`([mat, threshold])	Build the connectivity dictionary based on the given atomic overlap matrices.

Attributes¶

_env

esipy._env[source]¶

esipy.write_aoms(mol, mf, name, aom, ring=[], partition=None)[source]¶

Writes the input for the ESI-3D code from the AOMs.

Parameters

mol (PySCF instance) – Molecule object from PySCF.
mf (PySCF instance) – Calculation object from PySCF.
name (str) – Name of the calculation.
aom (list) – Concatenated list of Atomic Overlap Matrices (AOMs) in the MO basis.
ring (list of int, optional) – Connectivity of the atoms in the ring. Can be more than one ring as a list of lists.
partition (str, optional) – Partition scheme for the AOMs. Options are “mulliken”, “lowdin”, “meta-lowdin”, “nao”, “iao”.

Returns

None

Generates

A ‘_atomicfiles/’ directory with all the files created.
A ‘.int’ file for each atom with its corresponding AOM.
A ‘name.files’ file with a list of the names of the ‘.int’ files.
A ‘name.bad’ file with a standard input for the ESI-3D code.
A ‘name.wfx’ file with the occupancies for the ESI-3D code.

esipy.read_aoms(path='.')[source]¶

Reads the AOMs from ESIpy’s writeaoms() method or from an AIMAll calculation.

Parameters: path (str) – Path of the directory of the files.
Returns: The AOMs in ESIpy format stored in ‘ESI.aom’.
Return type: list

esipy.read_molinfo(path)[source]¶

Reads all *.int files from a directory and builds the molinfo dictionary.

Parameters: path (str) – Path to the directory containing *.int files.
Returns: A dictionary containing molecular information.
Return type: dict

esipy.compute_iring(arr, aom)[source]¶

Calculation of the Iring aromaticity index.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.

Returns

The Iring for the given ring connectivity.

Return type

float

esipy.sequential_mci(arr, aom, partition)[source]¶: Computes the MCI sequentially by computing the Iring without storing the permutations. Default option if no number of cores is specified.

esipy.multiprocessing_mci(arr, aom, ncores, partition)[source]¶: Computes the MCI by generating all the permutations for a later distribution along the specified number of cores.

esipy.compute_av1245(arr, aom, partition)[source]¶

Computes the AV1245 and AVmin indices. Not available for rings smaller than 6 members.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.
partition (str) – Specifies the atom-in-molecule partition scheme. Options include ‘mulliken’, ‘lowdin’, ‘meta-lowdin’, ‘nao’, and ‘iao’.

Returns

The AV1245 index, the AVmin index, and each of the AV1245 in a list for the output, respectively.

Return type

tuple

esipy.compute_pdi(arr, aom)[source]¶

Computes the PDI for the given 6-membered ring connectivity. Only computed for rings n=6.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.

Returns

The PDI value and each of the DIs in para position.

Return type

tuple

esipy.compute_flu(arr, molinfo, aom, flurefs=None, partition=None)[source]¶

Computes the FLU index.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
molinfo (dict) – Contains the molecular information.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.
flurefs (dict, optional) – User-provided references for the FLU index.
partition (str, optional) – Specifies the atom-in-molecule partition scheme. Options include ‘mulliken’, ‘lowdin’, ‘meta-lowdin’, ‘nao’, and ‘iao’.

Returns

The FLU value for the given ring connectivity.

Return type

float

esipy.compute_boa(arr, aom)[source]¶

Computes the BOA and BOA_c indices.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.

Returns

Contains the BOA and the BOA_c indices, respectively.

Return type

tuple

esipy.compute_homer(arr, molinfo, homerrefs=None)[source]¶

Computes the HOMER index.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
molinfo (dict) – Contains the molecular information.
homerrefs (dict, optional) – User-provided references for the HOMER index.

Returns

HOMER value for the given ring connectivity.

Return type

float

esipy.compute_homa(arr, molinfo, homarefs=None)[source]¶

Computes the HOMA index.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
molinfo (dict) – Contains the molecular information.
homarefs (dict, optional) – User-provided references for the HOMA index.

Returns

HOMA value for the given ring connectivity.

Return type

float

esipy.compute_bla(arr, molinfo)[source]¶

Computes the BLA and BLA_c indices.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
molinfo (dict) – Contains the molecular information.

Returns

Contains the BLA and the BLA_c indices, respectively.

Return type

tuple

esipy.compute_iring_no(arr, aom)[source]¶

Calculation of the Iring aromaticity index for correlated wavefunctions.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.

Returns

The Iring for the given ring connectivity.

Return type

float

esipy.sequential_mci_no(arr, aom, partition)[source]¶: Computes the MCI for correlated wavefunctions sequentially by computing the Iring without storing the permutations.

esipy.multiprocessing_mci_no(arr, aom, ncores, partition)[source]¶: Computes the MCI for correlated wavefunctions by generating all the permutations for a later distribution along the specified number of cores.

esipy.compute_av1245_no(arr, aom, partition)[source]¶

Computes the AV1245 and AVmin indices for correlated wavefunctions. Not available for rings smaller than 6 members.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.
partition (str) – Specifies the atom-in-molecule partition scheme. Options include ‘mulliken’, ‘lowdin’, ‘meta-lowdin’, ‘nao’, and ‘iao’.

Returns

The AV1245 index, the AVmin index, and each of the AV1245 in a list for the output, respectively.

Return type

tuple

esipy.compute_pdi_no(arr, aom)[source]¶

Computes the PDI for the given 6-membered ring connectivity. Only computed for rings n=6.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.

Returns

The PDI value and each of the DIs in para position.

Return type

tuple

esipy.compute_boa_no(arr, aom)[source]¶

Computes the BOA and BOA_c indices for correlated wavefunctions.

Parameters

arr (list of int) – Contains the indices defining the ring connectivity.
aom (list of matrices) – Specifies the Atomic Overlap Matrices (AOMs) in the MO basis.

Returns

Contains the BOA and the BOA_c indices, respectively.

Return type

tuple

esipy.make_aoms(mol, mf, partition, myhf=None, save=None)¶: Build the Atomic Overlap Matrices (AOMs) in the Molecular Orbitals basis.

esipy.mol_info(mol=None, mf=None, save=None, partition=None, connec=None)[source]¶

Obtains information from the molecule and the calculation to complement the main code function without requiring the ‘mol’ and ‘mf’ objects.

Parameters

mol (pyscf.gto.Mole) – PySCF Mole object.
mf (pyscf.scf.hf.SCF) – PySCF SCF object.
save (str) – String with the name of the file to save the information.
partition (str) – String with the name of the partition.

Returns

Dictionary with the information of the molecule and the calculation.

Return type

dict

esipy.format_partition(partition)[source]¶

esipy.load_file(file)[source]¶

Loads a variable from a file.

Parameters: file (str) – Contains the name or the path containing the variable.
Returns: The file loaded.
Return type: object

esipy.format_short_partition(partition)[source]¶

esipy.wf_type(aom)[source]¶

Checks the topology of the AOMs to obtain the type of wavefunction.

Parameters: aom – The Atomic Overlap Matrices (AOMs) in the MO basis.
Returns: A string with the type of wave function (‘rest’, ‘unrest’ or ‘no’).

esipy.save_file(file, save)[source]¶

Saves a variable to a file.

Parameters

file (object) – The variable to be stored.
save (str) – The name or the path where the variable will be saved.

Returns

None

esipy.build_connec_rest(Smo, thres=0.25)[source]¶

esipy.build_connec_unrest(Smo, thres=0.25)[source]¶

esipy.build_connec_no(Smo, thres=0.25)[source]¶

esipy.find_rings(connec, minlen=6, maxlen=6, exclude=None)[source]¶

esipy.process_fragments(aom, rings, done=False)[source]¶

Processes fragments by combining AOMs and updating rings.

Parameters

aom – List of AOMs.
rings – List of rings (can include sets for fragments).

Returns

Updated AOMs, rings, and fragment AOMs.

Return type

tuple (list, list, list)

esipy.build_connectivity(mat=None, threshold=0.25)[source]¶

Build the connectivity dictionary based on the given atomic overlap matrices.

Parameters

mat – Atomic overlap matrices. If None, uses self.aom or builds meta-lowdin AOMs
threshold – Threshold for connectivity determination. Default is 0.25.

Returns

Dictionary representing atomic connectivity

class esipy.IndicatorsRest(aom=None, rings=None, mol=None, mf=None, myhf=None, partition=None, mci=None, av1245=None, flurefs=None, homarefs=None, homerrefs=None, connectivity=None, geom=None, molinfo=None, ncores=1)[source]¶

property iring[source]¶

Compute the Iring value.

Returns: The Iring value :rtype: float

property mci[source]¶

Compute the MCI value.

Returns: The MCI value
Return type: float

property av1245[source]¶

Get the AV1245 value.

Returns: The AV1245 value.
Return type: float

property avmin[source]¶

Get the AVmin value.

Returns: The AVmin value.
Return type: float

property av1245_list[source]¶

Get the list of 4c-MCIs that form the AV1245.

Returns: The list of 4c-MCIs that form the AV1245.
Return type: numpy.ndarray

property pdi[source]¶

Get the PDI value.

Returns: The PDI value.
Return type: float

property pdi_list[source]¶

Get the list of the DIs (1-4, 2-5, 3-6).

Returns: The list of the DI values that form PDI.
Return type: numpy.ndarray

property flu[source]¶

Compute the FLU value.

Returns: The FLU value.
Return type: float

property boa[source]¶

Get the BOA value.

Returns: The BOA value.
Return type: float

property boa_c[source]¶

Get the BOA_c value.

Returns: The BOA_c value.
Return type: float

property homer[source]¶

Get the HOMER value.

Returns: The HOMER value.
Return type: float

property homa[source]¶

Get the HOMA value.

Returns: The HOMA value.
Return type: float

property en[source]¶

Get the EN value.

Returns: The EN value.
Return type: float

property geo[source]¶

Get the GEO value.

Returns: The GEO value.
Return type: float

property bla[source]¶

Get the BLA value.

Returns: The BLA value.
Return type: float

property bla_c[source]¶

Get the BLA_c value.

Returns: The BLA_c value.
Return type: float

_av()[source]¶

Compute the AV1245, AVmin and the list of the 4c-MCIs.

Returns: Tuple containing the AV1245, AVmin and the list of the 4c-MCIs.
Return type: tuple

_pdi()[source]¶

Compute the PDI.

Returns: The PDI value.
Return type: float

_boa()[source]¶

Compute the BOA and BOA_c values.

Returns: The BOA and BOA_c values.
Return type: tuple

_homa()[source]¶

Compute the HOMA and the EN and GEO components.

Returns: The HOMA, EN and GEO values.
Return type: tuple

_bla()[source]¶

Compute the BLA and BLA_c values.

Returns: The BLA and BLA_c values.
Return type: tuple

class esipy.IndicatorsUnrest(aom=None, rings=None, mol=None, mf=None, myhf=None, partition=None, mci=None, av1245=None, flurefs=None, homarefs=None, homerrefs=None, connectivity=None, geom=None, molinfo=None, ncores=1)[source]¶

Initialize the indicators from Unrestricted calculations.

Parameters

aom (concatenated list) – Atomic Overlap Matrices (AOMs) in the MO basis.
rings (list) – List of indices of the atoms in the ring connectivity. Can be a list of lists.
mol (optional, obj) – Molecule object “mol” from PySCF.
mf (optional, obj) – Calculation object “mf” from PySCF.
partition (optional, str) – Type of Hilbert-space partition scheme. Options are ‘mulliken’, ‘lowdin’, ‘meta-lowdin’, ‘nao’ and ‘iao’.
mci (optional, boolean) – Whether to compute the MCI.
av1245 (optional, boolean) – Whether to compute the AV1245.
flurefs (optional, dict) – Custom FLU references.
homarefs (optional, dict) – Custom HOMA references: “n_opt”, “c”, “r1”.
homerrefs (optional, dict) – Custom HOMER references: “alpha” and “r_opt” .
connectivity (optional, list) – Symbols of the ring connectivity as in “rings”.
geom (optional, list of lists) – Geometry of the molecule as in mol.atom_coords().
molinfo (optional, dict) – Information about the molecule and calculation.
ncores (optional, int) – Number of cores to use for the MCI calculation. Default is 1.

property iring[source]¶

Get the Iring value.

Returns: The Iring value.
Return type: float

property iring_alpha[source]¶

Get the Iring_alpha value.

Returns: The Iring_alpha value.
Return type: float

property iring_beta[source]¶

Get the Iring_beta value.

Returns: The Iring_beta value.
Return type: float

property mci[source]¶

Get the MCI value.

Returns: The MCI value.
Return type: float

property mci_alpha[source]¶

Get the MCI_alpha value.

Returns: The MCI_alpha value.
Return type: float

property mci_beta[source]¶

Get the MCI_beta value.

Returns: The MCI_beta value.
Return type: float

property av1245[source]¶

Get the AV1245 value.

Returns: The AV1245 value.
Return type: float

property av1245_alpha[source]¶

Get the AV1245_alpha value.

Returns: The AV1245_alpha value.
Return type: float

property av1245_beta[source]¶

Get the AV1245_beta value.

Returns: The AV1245_beta value.
Return type: float

property avmin[source]¶

Get the AVmin value.

Returns: The AVmin value.
Return type: float

property avmin_alpha[source]¶

Get the AVmin_alpha value.

Returns: The AVmin_alpha value.
Return type: float

property avmin_beta[source]¶

Get the AVmin_beta value.

Returns: The AVmin_beta value.
Return type: float

property av1245_list[source]¶

Get the list of 4c-MCIs that form the AV1245.

Returns: The list of 4c-MCIs that form the AV1245.
Return type: numpy.ndarray

property av1245_list_alpha[source]¶

Get the list of 4c-MCIs that form the AV1245_alpha.

Returns: The list of 4c-MCIs that form the AV1245_alpha.
Return type: numpy.ndarray

property av1245_list_beta[source]¶

Get the list of 4c-MCIs that form the AV1245_beta.

Returns: The list of 4c-MCIs that form the AV1245_beta.
Return type: numpy.ndarray

property pdi[source]¶

Get the PDI value.

Returns: The PDI value.
Return type: float

property pdi_alpha[source]¶

Get the PDI_alpha value.

Returns: The PDI_alpha value.
Return type: float

property pdi_beta[source]¶

Get the PDI_beta value.

Returns: The PDI_beta value.
Return type: float

property pdi_list[source]¶

Get the list of the DIs (1-4, 2-5, 3-6).

Returns: The list of the DI values that form PDI.
Return type: numpy.ndarray

property pdi_list_alpha[source]¶

Get the list of the alpha component of the DIs (1-4, 2-5, 3-6).

Returns: The list of the alpha component of the DI values that form PDI.
Return type: numpy.ndarray

property pdi_list_beta[source]¶

Get the list of the beta component of the DIs (1-4, 2-5, 3-6).

Returns: The list of the beta component of the DI values that form PDI.
Return type: numpy.ndarray

property flu[source]¶

Get the FLU value.

Returns: The FLU value.
Return type: float

property flu_alpha[source]¶

Get the FLU_alpha value.

Returns: The FLU_alpha value.
Return type: float

property flu_beta[source]¶

Get the FLU_beta value.

Returns: The FLU_beta value.
Return type: float

property boa[source]¶

Get the BOA value.

Returns: The BOA value.
Return type: float

property boa_alpha[source]¶

Get the BOA_alpha value.

Returns: The BOA_alpha value.
Return type: float

property boa_beta[source]¶

Get the BOA_beta value.

Returns: The BOA_beta value
Return type: float

property boa_c[source]¶

Get the BOA_c value.

Returns: The BOA_c value.
Return type: float

property boa_c_alpha[source]¶

Get the BOA_c_alpha value.

Returns: The BOA_c_alpha value.
Return type: float

property boa_c_beta[source]¶

Get the BOA_c_beta value.

Returns: The BOA_c_beta value.
Return type: float

property homa[source]¶

Get the HOMA value.

Returns: The HOMA value.
Return type: float

property en[source]¶

Get the EN value.

Returns: The EN value.
Return type: float

property geo[source]¶

Get the GEO value.

Returns: The GEO value.
Return type: float

property homer[source]¶

Get the HOMER value.

Returns: The HOMER value.
Return type: float

property bla[source]¶

Get the BLA value.

Returns: The BLA value.
Return type: float

property bla_c[source]¶

Get the BLA_c value.

Returns: The BLA_c value.
Return type: float

_irings()[source]¶

Compute the Iring and their alpha and beta components.

Returns: The Iring, Iring_alpha and Iring_beta.
Return type: tuple

_mcis()[source]¶

Compute the MCI values for alpha and beta components. Different algorithms are used depending on: the number of cores.

Returns: The MCI values for alpha and beta components.
Return type: tuple

_avs()[source]¶

Compute the AV1245, AVmin and the list of the 4c-MCIs for alpha and beta components.

Returns: The AV1245, AVmin and the list of the 4c-MCIs for alpha and beta components.
Return type: tuple

_pdis()[source]¶

Compute the PDI values for alpha and beta components.

Returns: The PDI values for alpha and beta components.
Return type: tuple

_flus()[source]¶

Compute the FLU values for alpha and beta components.

Returns: The FLU values for alpha and beta components.
Return type: tuple

_boas()[source]¶

Compute the BOA and BOA_c values for alpha and beta components.

Returns: The BOA and BOA_c values for alpha and beta components.
Return type: tuple

_homas()[source]¶

Compute the HOMA and the EN and GEO components.

Returns: The HOMA, EN and GEO values.
Return type: tuple

_blas()[source]¶

Compute the BLA and BLA_c values.

Returns: The BLA and BLA_c values.
Return type: tuple

class esipy.IndicatorsNatorb(aom=None, rings=None, mol=None, mf=None, myhf=None, partition=None, mci=None, av1245=None, flurefs=None, homarefs=None, homerrefs=None, connectivity=None, geom=None, molinfo=None, ncores=1)[source]¶

Initialize the indicators from Natural Orbitals calculations.

Parameters

aom (concatenated list) – Atomic Overlap Matrices (AOMs) in the MO basis.
rings (list) – List of indices of the atoms in the ring connectivity. Can be a list of lists.
mol (optional, obj) – Molecule object “mol” from PySCF.
mf (optional, obj) – Calculation object “mf” from PySCF.
myhf (optional, obj) – Reference RHF object for IAO-Natural Orbitals calculation.
partition (optional, str) – Type of Hilbert-space partition scheme. Options are ‘mulliken’, ‘lowdin’, ‘meta-lowdin’, ‘nao’ and ‘iao’.
mci (optional, boolean) – Whether to compute the MCI.
av1245 (optional, boolean) – Whether to compute the AV1245.
flurefs (optional, dict) – Custom FLU references.
homarefs (optional, dict) – Custom HOMA references: “n_opt”, “c”, “r1”.
homerrefs (optional, dict) – Custom HOMER references: “alpha” and “r_opt” .
connectivity (optional, list) – Symbols of the ring connectivity as in “rings”.
geom (optional, list of lists) – Geometry of the molecule as in mol.atom_coords().
molinfo (optional, dict) – Information about the molecule and calculation.
ncores (optional, int) – Number of cores to use for the MCI calculation. Default is 1.

property iring[source]¶

Compute the Iring value.

Returns: The Iring value.
Return type: float

property mci[source]¶

Compute the MCI value.

Returns: The MCI value.
Return type: float

property av1245[source]¶

Get the AV1245 value.

Returns: The AV1245 value
Return type: float

property avmin[source]¶

Get the AVmin value.

Returns: The AVmin value.
Return type: float

property av1245_list[source]¶

Get the list of 4c-MCIs that form the AV1245.

Returns: The list of 4c-MCIs that form the AV1245.
Return type: numpy.ndarray

property pdi[source]¶

Get the PDI value.

Returns: The PDI value.
Return type: float

property pdi_list[source]¶

Get the list of the DIs (1-4, 2-5, 3-6).

Returns: The list of the DI values that form PDI.
Return type: numpy.ndarray

property flu[source]¶

Compute the FLU value.

Returns: The FLU value.
Return type: float

property boa[source]¶

Get the BOA value.

Returns: The BOA value.
Return type: float

property boa_c[source]¶

Get the BOA_c value.

Returns: The BOA_c value.
Return type: float

property homer[source]¶

Get the HOMER value.

Returns: The HOMER value.
Return type: float

property homa[source]¶

Get the HOMA value.

Returns: The HOMA value.
Return type: float

property en[source]¶

Get the EN value.

Returns: The EN value.
Return type: float

property geo[source]¶

Get the GEO value.

Returns: The GEO value.
Return type: float

property homer[source]¶

Get the HOMER value.

Returns: The HOMER value.
Return type: float

property bla[source]¶

Get the BLA value.

Returns: The BLA value.
Return type: float

property bla_c[source]¶

Get the BLA_c value.

Returns: The BLA_c value.
Return type: float

_av_no()[source]¶

Compute the AV1245, AVmin and the list of the 4c-MCIs.

Returns: List containing the AV1245, AVmin and the list of the 4c-MCIs.
Return type: list

_pdi_no()[source]¶

Compute the PDI.

Returns: The PDI value.
Return type: float

_boa_no()[source]¶

Compute the BOA and BOA_c values.

Returns: The BOA and BOA_c values.
Return type: tuple

_homas()[source]¶

Compute the HOMA and the EN and GEO components.

Returns: The HOMA, EN and GEO values.
Return type: tuple

_blas()[source]¶

Compute the BLA and BLA_c values.

Returns: The BLA and BLA_c values.
Return type: tuple

class esipy.ESI(aom=None, rings=None, mol=None, mf=None, myhf=None, partition=None, mci=None, av1245=None, flurefs=None, homarefs=None, homerrefs=None, connectivity=None, geom=None, molinfo=None, ncores=1, save=None, readpath='.', read=False, maxlen=12, minlen=6, rings_thres=0.3, exclude=None)[source]¶

Main class for the ESIpy code.

Attributes: aom (concatenated list): Atomic Overlap Matrices (AOMs) in the MO basis. rings (list): List of indices of the atoms in the ring connectivity. Can be a list of lists. mol (optional, obj): Molecule object “mol” from PySCF. mf (optional, obj): Calculation object “mf” from PySCF. myhf (optional, obj): Reference RHF object for IAO-Natural Orbitals calculation. partition (optional, str): Type of Hilbert-space partition scheme.

Options are ‘mulliken’, ‘lowdin’, ‘meta-lowdin’, ‘nao’ and ‘iao’.

mci (optional, boolean): Whether to compute the MCI. av1245 (optional, boolean): Whether to compute the AV1245. flurefs (optional, dict): Custom FLU references. homarefs (optional, dict): Custom HOMA references: “n_opt”, “c”, “r1”. homerrefs (optional, dict): Custom HOMER references: “alpha” and “r_opt” . connectivity (optional, list): Symbols of the ring connectivity as in “rings”. geom (optional, list of lists): Geometry of the molecule as in mol.atom_coords(). molinfo (optional, dict): Information about the molecule and calculation. ncores (optional, int): Number of cores to use for the MCI calculation. Default is 1. saveaoms (optional): Name where to save the AOMs in binary. savemolinfo (optional): Name where to save the molecular information dictionary in binary. readpath (optional, str): Path to read the AOMs. Default is ‘.’. indicators (obj): Object containing the indicators of the calculation. Generated in the initialization.

Methods: readaoms(): Reads the AOMs from a directory in AIMAll and ESIpy format. writeaoms(): Writes ESIpy’s AOMs in AIMAll format. print(): Prints the output for the main ESIpy functions.

property rings[source]¶

property molinfo[source]¶

Get the information about the molecule and calculation. If not provided, it will compute it. If set as a string, it will read the information from the directory. Can be saved in a file with the savemolinfo attribute.

Returns: Information about the molecule and calculation.
Return type: dict

property aom[source]¶

Get the Atomic Overlap Matrices (AOMs) in the MO basis. If not provided, it will compute them. If set as a string, it will read the AOMs from the directory. Can be saved in a file with the saveaoms attribute.

Returns: The AOMs in the MO basis.
Return type: list

property partition[source]¶

Get the partition scheme for the Hilbert-space. Options are ‘mulliken’, ‘lowdin’, ‘meta-lowdin’, ‘nao’ and ‘iao’. Some variations of these names are also available. Only one partition at a time.

Returns: The partition scheme for the Hilbert-space calculation.
Return type: str

property connec[source]¶

Get the connectivity matrix. If the partition is ‘mulliken’ or ‘lowdin’, build the NAO AOMs and compute the connectivity matrix from there. The computation is controlled by the ‘done_connec’ flag. Based on the DIs.

Returns: The connectivity matrix.
Return type: dict

property mci[source]¶

Whether to compute the MCI. If not provided, it will compute it if the number of rings is less than 12.

Returns: Whether to compute the MCI.
Return type: boolean

property exclude[source]¶: Processes the exclude list. If an element symbol (str) is found, it finds all indices for that element. If an int is found, it keeps it.

property av1245[source]¶

Whether to compute the AV1245. If not provided, it will compute it if the number of rings is greater than 9.

Returns: Whether to compute the AV1245.
Return type: boolean

readaoms()[source]¶

Reads the AOMs from a directory in AIMAll and ESIpy format. Overwrites ‘ESI.aom’ variable. By default, it will read the AOMs from the working directory. If the ‘readpath’ attribute is set, it will read from that directory.

Returns: The AOMs in the MO basis, overwriting the aom variable.
Return type: list

writeaoms(file)[source]¶

Writes ESIpy’s AOMs in AIMAll format in the working directory.

Generates:

A ‘_atomicfiles/’ directory with all the files created.
A ‘.int’ file for each atom with its corresponding AOM.
A ‘name.files’ with a list of the names of the ‘.int’ files.
A ‘name.bad’ with a standard input for the ESI-3D code.
A ‘name.wfx’ with the occupancies for the ESI-3D code.

print()[source]¶: Main output for ESIpy. Population analysis, localization and delocalization indices and electronic (and geometric) aromaticity indicators.

esipy¶

Submodules¶

Package Contents¶

Classes¶

Functions¶

Attributes¶

`esipy`¶