vayesta.core.bath

Submodules

vayesta.core.bath.bath

Bath base class.

class vayesta.core.bath.bath.Bath(fragment)

Bases: object

property spin_restricted

property spin_unrestricted

property spinsym

property mf

property mol

property log

property base

property c_frag

vayesta.core.bath.bno

class vayesta.core.bath.bno.BNO_Threshold(type, threshold)

Bases: object

get_number(bno_occup, electron_total=None)

Get number of BNOs.

class vayesta.core.bath.bno.BNO_Bath(fragment, dmet_bath, occtype, *args, c_buffer=None, canonicalize=True, **kwargs)

Bases: Bath

Bath natural orbital (BNO) bath, requires DMET bath.

property c_cluster_occ

Occupied DMET cluster orbitals.

property c_cluster_vir

Virtual DMET cluster orbitals.

make_bno_coeff(*args, **kwargs)

property c_env

property ncluster

kernel()

log_histogram(n_bno)

get_bath(bno_threshold=None, **kwargs)

get_finite_bath_correction(c_active, c_frozen)

truncate_bno(coeff, occup, bno_threshold=None, verbose=True)

Split natural orbitals (NO) into bath and rest.

get_active_space(c_active=None)

property base

property c_frag

property log

property mf

property mol

property spin_restricted

property spin_unrestricted

property spinsym

class vayesta.core.bath.bno.BNO_Bath_UHF(fragment, dmet_bath, occtype, *args, c_buffer=None, canonicalize=True, **kwargs)

Bases: BNO_Bath

property ncluster

log_histogram(n_bno)

truncate_bno(coeff, occup, *args, **kwargs)

Split natural orbitals (NO) into bath and rest.

property base

property c_cluster_occ

Occupied DMET cluster orbitals.

property c_cluster_vir

Virtual DMET cluster orbitals.

property c_env

property c_frag

get_active_space(c_active=None)

get_bath(bno_threshold=None, **kwargs)

get_finite_bath_correction(c_active, c_frozen)

kernel()

property log

make_bno_coeff(*args, **kwargs)

property mf

property mol

property spin_restricted

property spin_unrestricted

property spinsym

class vayesta.core.bath.bno.MP2_BNO_Bath(*args, project_dmet_order=0, project_dmet_mode='full', project_dmet=None, **kwargs)

Bases: BNO_Bath

get_eris_or_cderi(actspace)

make_delta_dm1(t2, actspace)

Delta MP2 density matrix

make_bno_coeff(eris=None)

Construct MP2 bath natural orbital coefficients and occupation numbers.

This routine works for both for spin-restricted and unrestricted.

Parameters:

eris (mp2._ChemistERIs) –

Returns:

• c_bno ((n(AO), n(BNO)) array) – Bath natural orbital coefficients.

• n_bno ((n(BNO)) array) – Bath natural orbital occupation numbers.

property base

property c_cluster_occ

Occupied DMET cluster orbitals.

property c_cluster_vir

Virtual DMET cluster orbitals.

property c_env

property c_frag

get_active_space(c_active=None)

get_bath(bno_threshold=None, **kwargs)

get_finite_bath_correction(c_active, c_frozen)

kernel()

property log

log_histogram(n_bno)

property mf

property mol

property ncluster

property spin_restricted

property spin_unrestricted

property spinsym

truncate_bno(coeff, occup, bno_threshold=None, verbose=True)

Split natural orbitals (NO) into bath and rest.

class vayesta.core.bath.bno.UMP2_BNO_Bath(*args, project_dmet_order=0, project_dmet_mode='full', project_dmet=None, **kwargs)

Bases: MP2_BNO_Bath, BNO_Bath_UHF

make_delta_dm1(t2, actspace)

Delta MP2 density matrix

property base

property c_cluster_occ

Occupied DMET cluster orbitals.

property c_cluster_vir

Virtual DMET cluster orbitals.

property c_env

property c_frag

get_active_space(c_active=None)

get_bath(bno_threshold=None, **kwargs)

get_eris_or_cderi(actspace)

get_finite_bath_correction(c_active, c_frozen)

kernel()

property log

log_histogram(n_bno)

make_bno_coeff(eris=None)

Construct MP2 bath natural orbital coefficients and occupation numbers.

This routine works for both for spin-restricted and unrestricted.

Parameters:

eris (mp2._ChemistERIs) –

Returns:

• c_bno ((n(AO), n(BNO)) array) – Bath natural orbital coefficients.

• n_bno ((n(BNO)) array) – Bath natural orbital occupation numbers.

property mf

property mol

property ncluster

property spin_restricted

property spin_unrestricted

property spinsym

truncate_bno(coeff, occup, *args, **kwargs)

Split natural orbitals (NO) into bath and rest.

vayesta.core.bath.dmet

class vayesta.core.bath.dmet.DMET_Bath_RHF(fragment, dmet_threshold=1e-06)

Bases: Bath

get_cluster_electrons()

Number of cluster electrons.

get_occupied_bath(*args, **kwargs)

Inherited bath classes can overwrite this to return additional occupied bath orbitals.

get_virtual_bath(*args, **kwargs)

Inherited bath classes can overwrite this to return additional virtual bath orbitals.

kernel()

get_environment()

make_dmet_bath(c_env, dm1=None, c_ref=None, nbath=None, verbose=True, reftol=0.8)

Calculate DMET bath, occupied environment and virtual environment orbitals.

If c_ref is not None, complete DMET orbital space using active transformation of reference orbitals.

TODO: * reftol should not be necessary - just determine how many DMET bath orbital N are missing from C_ref and take the N largest eigenvalues over the combined occupied and virtual eigenvalues.

Parameters:

• c_env ((n(AO), n(env)) array) – MO-coefficients of environment orbitals.

• dm1 ((n(AO), n(AO)) array, optional) – Mean-field one-particle reduced density matrix in AO representation. If None, self.mf.make_rdm1() is used. Default: None.

• c_ref (ndarray, optional) – Reference DMET bath orbitals from previous calculation.

• nbath (int, optional) – Number of DMET bath orbitals. If set, the parameter tol is ignored. Default: None.

• tol (float, optional) – Tolerance for DMET orbitals in eigendecomposition of density-matrix. Default: 1e-5.

• reftol (float, optional) – Tolerance for DMET orbitals in projection of reference orbitals.

Returns:

• c_bath ((n(AO), n(bath)) array) – DMET bath orbitals.

• eig (n(bath) array) – DMET orbital occupation numbers (in [0,1]).

• c_occenv ((n(AO), n(occ. env)) array) – Occupied environment orbitals.

• c_virenv ((n(AO), n(vir. env)) array) – Virtual environment orbitals.

make_dmet_bath_fast(c_env, dm1=None)

Fast DMET orbitals. from Ref. J. Chem. Phys. 151, 064108 (2019); https://doi.org/10.1063/1.5108818

Problem: How to get C_occenv and C_virenv without N^3 diagonalization?

log_info(eig, c_env, threshold=1e-10)

use_ref_orbitals(c_bath, c_occenv, c_virenv, c_ref, reftol=0.8)

Not maintained!

property base

property c_frag

property log

property mf

property mol

property spin_restricted

property spin_unrestricted

property spinsym

class vayesta.core.bath.dmet.DMET_Bath_UHF(fragment, dmet_threshold=1e-06)

Bases: DMET_Bath_RHF

get_cluster_electrons()

Number of (alpha, beta) cluster electrons.

get_occupied_bath(*args, **kwargs)

Inherited bath classes can overwrite this to return additional occupied bath orbitals.

get_virtual_bath(*args, **kwargs)

Inherited bath classes can overwrite this to return additional virtual bath orbitals.

make_dmet_bath(c_env, dm1=None, **kwargs)

Calculate DMET bath, occupied environment and virtual environment orbitals.

If c_ref is not None, complete DMET orbital space using active transformation of reference orbitals.

TODO: * reftol should not be necessary - just determine how many DMET bath orbital N are missing from C_ref and take the N largest eigenvalues over the combined occupied and virtual eigenvalues.

Parameters:

• c_env ((n(AO), n(env)) array) – MO-coefficients of environment orbitals.

• dm1 ((n(AO), n(AO)) array, optional) – Mean-field one-particle reduced density matrix in AO representation. If None, self.mf.make_rdm1() is used. Default: None.

• c_ref (ndarray, optional) – Reference DMET bath orbitals from previous calculation.

• nbath (int, optional) – Number of DMET bath orbitals. If set, the parameter tol is ignored. Default: None.

• tol (float, optional) – Tolerance for DMET orbitals in eigendecomposition of density-matrix. Default: 1e-5.

• reftol (float, optional) – Tolerance for DMET orbitals in projection of reference orbitals.

Returns:

• c_bath ((n(AO), n(bath)) array) – DMET bath orbitals.

• eig (n(bath) array) – DMET orbital occupation numbers (in [0,1]).

• c_occenv ((n(AO), n(occ. env)) array) – Occupied environment orbitals.

• c_virenv ((n(AO), n(vir. env)) array) – Virtual environment orbitals.

property base

property c_frag

get_environment()

kernel()

property log

log_info(eig, c_env, threshold=1e-10)

make_dmet_bath_fast(c_env, dm1=None)

Fast DMET orbitals. from Ref. J. Chem. Phys. 151, 064108 (2019); https://doi.org/10.1063/1.5108818

Problem: How to get C_occenv and C_virenv without N^3 diagonalization?

property mf

property mol

property spin_restricted

property spin_unrestricted

property spinsym

use_ref_orbitals(c_bath, c_occenv, c_virenv, c_ref, reftol=0.8)

Not maintained!

vayesta.core.bath.ewdmet

class vayesta.core.bath.ewdmet.EwDMET_Bath_RHF(fragment, dmet_bath, occtype, *args, threshold=None, max_order=20, **kwargs)

Bases: Bath

get_fock(*args, **kwargs)

kernel()

property c_env

get_bath(order)

property base

property c_frag

property log

property mf

property mol

property spin_restricted

property spin_unrestricted

property spinsym

vayesta.core.bath.full

class vayesta.core.bath.full.Full_Bath_RHF(fragment, dmet_bath, occtype, *args, **kwargs)

Bases: Bath

property c_env

get_bath(*args, **kwargs)

property base

property c_frag

property log

property mf

property mol

property spin_restricted

property spin_unrestricted

property spinsym

class vayesta.core.bath.full.Full_Bath_UHF(fragment, dmet_bath, occtype, *args, **kwargs)

Bases: Full_Bath_RHF

get_bath(*args, **kwargs)

property base

property c_env

property c_frag

property log

property mf

property mol

property spin_restricted

property spin_unrestricted

property spinsym

vayesta.core.bath.helper

vayesta.core.bath.helper.make_histogram(values, bins, labels=None, binwidth=5, height=6, fill=':', show_number=False, invertx=True, rstrip=True)

vayesta.core.bath.helper.make_horizontal_histogram(values, bins=None, maxbarlength=50, invertx=True)

vayesta.core.bath.helper.transform_mp2_eris(eris, c_occ, c_vir, ovlp)

Transform eris of kind (ov|ov) (occupied-virtual-occupied-virtual)

OBSOLETE: replaced by transform_eris

vayesta.core.bath.r2bath

class vayesta.core.bath.r2bath.R2_Bath_RHF(fragment, dmet_bath, occtype, *args, **kwargs)

Bases: Bath

property c_env

get_r2()

kernel()

get_bath(rcut, unit='Ang')

log_histogram(r, name)

property base

property c_frag

property log

property mf

property mol

property spin_restricted

property spin_unrestricted

property spinsym

vayesta.core.bath.rpa

class vayesta.core.bath.rpa.RPA_BNO_Bath(*args, project_dmet_order=0, project_dmet_mode='full', project_dmet=None, **kwargs)

Bases: BNO_Bath

make_bno_coeff(cderis=None)

Construct RPA bath natural orbital coefficients and occupation numbers.

This routine works for both for spin-restricted and unrestricted.

Parameters:

cderis (cderis in the particle-hole space.) –

Returns:

• c_bno ((n(AO), n(BNO)) array) – Bath natural orbital coefficients.

• n_bno ((n(BNO)) array) – Bath natural orbital occupation numbers.

property base

property c_cluster_occ

Occupied DMET cluster orbitals.

property c_cluster_vir

Virtual DMET cluster orbitals.

property c_env

property c_frag

get_active_space(c_active=None)

get_bath(bno_threshold=None, **kwargs)

get_finite_bath_correction(c_active, c_frozen)

kernel()

property log

log_histogram(n_bno)

property mf

property mol

property ncluster

property spin_restricted

property spin_unrestricted

property spinsym

truncate_bno(coeff, occup, bno_threshold=None, verbose=True)

Split natural orbitals (NO) into bath and rest.

Module contents

vayesta.core.bath.DMET_Bath(fragment, *args, **kwargs)

vayesta.core.bath.EwDMET_Bath(fragment, *args, **kwargs)

vayesta.core.bath.MP2_Bath(fragment, *args, **kwargs)

vayesta.core.bath.RPA_Bath(fragment, *args, **kwargs)

vayesta.core.bath.R2_Bath(fragment, *args, **kwargs)

vayesta.core.bath.Full_Bath(fragment, *args, **kwargs)