wavefunction_analysis.embedding package

Submodules

wavefunction_analysis.embedding.fci_thermal module

wavefunction_analysis.embedding.fragment_entangle module

class EmbeddingMeanField(mf, frgm_list, extra_orb=0)

Bases: object

emb_basis_dmet(mf, ifrgm, embed_method=0)

build embedding basis for a given fragment

get_eomf(mf)

get the embedding mean-field object with reduced mo space ready to be used for excited-state calculations ———————————————————————– returns: eomf: embedding mf object

fragment_localization(mf, frgm_list, extra_orb=0)

get the localized orbitals and density matrix for fragment analysis

get_embedding_energy(mf, coeff_eo_in_ao, dm_eo_in_ao, neo_imp, extra_orb=0)

electronic energy of the impurity in the embedding basis

get_embedding_orbital(dm_lo_in_ao, coeff_lo_in_ao, ovlp_ao, imp_lo_idx, env_lo_idx, method=0, threshold=1e-12)

embedding orbital construction from the density matrix in local orbital basis method=0: singular value vectors of off-diagonal block of the dm in lo method=1: eigenvectors of environment diagonal block of the dm in lo ———————————————————————- returns: coeff_eo_in_ao: embedding orbital coefficients in ao basis dm_eo_in_ao: density matrix in embedding orbital basis

get_embedding_system(mf, frgm_idx, ifrgm=0, extra_orb=0)

embedding energy calculation for a given fragment mf: pyscf mean-field object frgm_idx: list of list of atomic indices for each fragment ifrgm: index of the fragment to be treated as impurity; if -1, loop over all fragments extra_orb: number of extra orbitals to include in the density matrix (can be negative) ————————————————————————– returns: energy: embedded energy of the impurity fragment

get_localized_orbital(mol, coeff, method='pipek_mezey')

get_localized_orbital_rdm(coeff_lo_in_ao, coeff_mo_in_ao, ovlp_ao, nocc, scale=2.0, extra_orb=0)

total density matrix alpha+beta in local orbital basis S^{1/2} P S^{1/2} = C_lo^T S C_mo occ C_mo occ^T S C_lo

wavefunction_analysis.embedding.mol_lo_tools module

lo_weight_on_ao(mol: Mole = None, coeff_ao_lo: ndarray = None, ovlp_ao: ndarray = None)

A function to calculate the weight of local orbitals on atomic orbitals.

Parameters:

• mol – pyscf.gto.Mole The molecule object.

• coeff_ao_lo – numpy.ndarray The coefficient matrix to transform atomic orbitals to local orbitals.

• ovlp_ao – numpy.ndarray The overlap matrix of atomic orbitals.

Returns:

numpy.ndarray

The weight of local orbitals on atomic orbitals.

Return type:

w2_ao_lo

lo_weight_on_atom(mol: Mole, coeff_ao_lo: ndarray = None, ovlp_ao: ndarray = None)

A function to calculate the weight of local orbitals on atomic orbitals.

Parameters:

• mol – pyscf.gto.Mole The molecule object.

• coeff_ao_lo – numpy.ndarray The coefficient matrix to transform atomic orbitals to local orbitals.

• ovlp_ao – numpy.ndarray The overlap matrix of atomic orbitals.

Returns:

numpy.ndarray

The weight of local orbitals on each atom.

Return type:

w2_atm_lo

lo_weight_on_frag(frag_atms_list: list, mol: Mole, coeff_ao_lo: ndarray = None, ovlp_ao: ndarray = None)

A function to calculate the weight of local orbitals on fragments.

Parameters:

• frag_atms_list – list A list of atoms in each fragment.

• mol – pyscf.gto.Mole The molecule object.

• coeff_ao_lo – numpy.ndarray The coefficient matrix to transform atomic orbitals to local orbitals.

• ovlp_ao – numpy.ndarray The overlap matrix of atomic orbitals.

Returns:

numpy.ndarray

The weight of local orbitals on each fragment.

Return type:

w2_frag_lo

partition_lo_to_atms(mol: Mole = None, coeff_ao_lo: ndarray = None, w2_atm_lo: ndarray = None, min_weight: float = 0.9)

A function to partition local orbitals to atoms.

Parameters:

• mol – pyscf.gto.Mole The molecule object.

• coeff_ao_lo – numpy.ndarray The coefficient matrix to transform atomic orbitals to local orbitals.

• w2_atm_lo – numpy.ndarray The weight of local orbitals on each atom.

• min_weight – float The minimum weight of local orbitals on each atom. If the max weight is smaller than min_weight, the local orbital will not be assigned to the atom.

Returns:

list

The list of local orbital indices on each atom.

Return type:

lo_idx_on_atm_list

partition_lo_to_frags(frag_atms_list: list, mol: Mole = None, coeff_ao_lo: ndarray = None, w2_frag_lo: ndarray = None, min_weight: float = 0.9)

A function to partition local orbitals to fragments.

Parameters:

• frag_atms_list – list The list of atoms in each fragment.

• mol – pyscf.gto.Mole The molecule object.

• coeff_ao_lo – numpy.ndarray The coefficient matrix to transform atomic orbitals to local orbitals.

• w2_frag_lo – numpy.ndarray The weight of local orbitals on each atom.

• min_weight – float The minimum weight of local orbitals on each atom. If the max weight is smaller than min_weight, the local orbital will not be assigned to the atom.

Returns:

list

The list of local orbital indices on each fragment.

Return type:

lo_idx_on_frag_list

partition_lo_to_imps(frag_atms_list: list, mol: Mole = None, coeff_ao_lo: ndarray = None, w2_frag_lo: ndarray = None, min_weight: float = 0.9)

A function to partition local orbitals to fragments.

Parameters:

• frag_atms_list – list The list of atoms in each fragment.

• mol – pyscf.gto.Mole The molecule object.

• coeff_ao_lo – numpy.ndarray The coefficient matrix to transform atomic orbitals to local orbitals.

• w2_frag_lo – numpy.ndarray The weight of local orbitals on each atom.

• min_weight – float The minimum weight of local orbitals on each atom. If the max weight is smaller than min_weight, the local orbital will not be assigned to the atom.

Returns:

list

The list of local orbital indices on each fragment.

Return type:

lo_idx_on_frag_list

wavefunction_analysis.embedding.orbital_entropy module

get_1rdm(c0, c2)

get_2rdm(c0, c2)

get_orbital_entropy_info(s1, s2, imethod=0)

get_rdm_entropy(rho)

normalize_wf(t2)

wavefunction_analysis.embedding.td_embeddinng module

Module contents