pyscf.mp package

Submodules

pyscf.mp.dfmp2 module

density fitting MP2, 3-center integrals incore.

class pyscf.mp.dfmp2.DFMP2(mf, frozen=None, mo_coeff=None, mo_occ=None)

Bases: pyscf.mp.mp2.MP2

ao2mo(mo_coeff=None)

init_amps(mo_energy=None, mo_coeff=None, eris=None, with_t2=True)

loop_ao2mo(mo_coeff, nocc)

make_rdm1(t2=None, ao_repr=False)

Spin-traced one-particle density matrix. The occupied-virtual orbital response is not included.

dm1[p,q] = <q_alpha^dagger p_alpha> + <q_beta^dagger p_beta>

The convention of 1-pdm is based on McWeeney’s book, Eq (5.4.20). The contraction between 1-particle Hamiltonian and rdm1 is E = einsum(‘pq,qp’, h1, rdm1)

Kwargs:

ao_reprboolean

Whether to transfrom 1-particle density matrix to AO representation.

make_rdm2(t2=None, ao_repr=False)

Spin-traced two-particle density matrix in MO basis

dm2[p,q,r,s] = sum_{sigma,tau} <p_sigma^dagger r_tau^dagger s_tau q_sigma>

Note the contraction between ERIs (in Chemist’s notation) and rdm2 is E = einsum(‘pqrs,pqrs’, eri, rdm2)

nuc_grad_method()

reset(mol=None)

update_amps(t2, eris)

Update non-canonical MP2 amplitudes

pyscf.mp.dfmp2.MP2

alias of pyscf.mp.dfmp2.DFMP2

pyscf.mp.dfmp2.kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=True, verbose=3)

pyscf.mp.gmp2 module

GMP2 in spin-orbital form E(MP2) = 1/4 <ij||ab><ab||ij>/(ei+ej-ea-eb)

class pyscf.mp.gmp2.GMP2(mf, frozen=None, mo_coeff=None, mo_occ=None)

Bases: pyscf.mp.mp2.MP2

ao2mo(mo_coeff=None)

energy(t2, eris)

MP2 energy

init_amps(mo_energy=None, mo_coeff=None, eris=None, with_t2=True)

make_rdm1(t2=None, ao_repr=False)

One-particle density matrix in the molecular spin-orbital representation (the occupied-virtual blocks from the orbital response contribution are not included).

dm1[p,q] = <q^dagger p> (p,q are spin-orbitals)

The convention of 1-pdm is based on McWeeney’s book, Eq (5.4.20). The contraction between 1-particle Hamiltonian and rdm1 is E = einsum(‘pq,qp’, h1, rdm1)

make_rdm2(t2=None, ao_repr=False)

Two-particle density matrix in the molecular spin-orbital representation

dm2[p,q,r,s] = <p^dagger r^dagger s q>

where p,q,r,s are spin-orbitals. p,q correspond to one particle and r,s correspond to another particle. The contraction between ERIs (in Chemist’s notation) and rdm2 is E = einsum(‘pqrs,pqrs’, eri, rdm2)

nuc_grad_method()

update_amps(t2, eris)

Update non-canonical MP2 amplitudes

pyscf.mp.gmp2.MP2

alias of pyscf.mp.gmp2.GMP2

pyscf.mp.gmp2.energy(mp, t2, eris)

MP2 energy

pyscf.mp.gmp2.kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=True, verbose=None)

pyscf.mp.gmp2.make_rdm1(mp, t2=None, ao_repr=False)

One-particle density matrix in the molecular spin-orbital representation (the occupied-virtual blocks from the orbital response contribution are not included).

dm1[p,q] = <q^dagger p> (p,q are spin-orbitals)

The convention of 1-pdm is based on McWeeney’s book, Eq (5.4.20). The contraction between 1-particle Hamiltonian and rdm1 is E = einsum(‘pq,qp’, h1, rdm1)

pyscf.mp.gmp2.make_rdm2(mp, t2=None, ao_repr=False)

Two-particle density matrix in the molecular spin-orbital representation

dm2[p,q,r,s] = <p^dagger r^dagger s q>

where p,q,r,s are spin-orbitals. p,q correspond to one particle and r,s correspond to another particle. The contraction between ERIs (in Chemist’s notation) and rdm2 is E = einsum(‘pqrs,pqrs’, eri, rdm2)

pyscf.mp.gmp2.update_amps(mp, t2, eris)

Update non-canonical MP2 amplitudes

pyscf.mp.mp2 module

RMP2

class pyscf.mp.mp2.MP2(mf, frozen=None, mo_coeff=None, mo_occ=None)

Bases: pyscf.lib.misc.StreamObject

restricted MP2 with canonical HF and non-canonical HF reference

Attributes:

verboseint

Print level. Default value equals to Mole.verbose

max_memoryfloat or int

Allowed memory in MB. Default value equals to Mole.max_memory

conv_tolfloat

For non-canonical MP2, converge threshold for MP2 correlation energy. Default value is 1e-7.

conv_tol_normtfloat

For non-canonical MP2, converge threshold for norm(t2). Default value is 1e-5.

max_cycleint

For non-canonical MP2, max number of MP2 iterations. Default value is 50.

diis_spaceint

For non-canonical MP2, DIIS space size in MP2 iterations. Default is 6.

level_shiftfloat

A shift on virtual orbital energies to stablize the MP2 iterations.

frozenint or list

If integer is given, the inner-most orbitals are excluded from MP2 amplitudes. Given the orbital indices (0-based) in a list, both occupied and virtual orbitals can be frozen in MP2 calculation.

>>> mol = gto.M(atom = 'H 0 0 0; F 0 0 1.1', basis = 'ccpvdz')
>>> mf = scf.RHF(mol).run()
>>> # freeze 2 core orbitals
>>> pt = mp.MP2(mf).set(frozen = 2).run()
>>> # freeze 2 core orbitals and 3 high lying unoccupied orbitals
>>> pt.set(frozen = [0,1,16,17,18]).run()

Saved results

e_corrfloat

MP2 correlation correction

e_totfloat

Total MP2 energy (HF + correlation)

t2 :

T amplitudes t2[i,j,a,b] (i,j in occ, a,b in virt)

Gradients(*args, **kwargs)

ao2mo(mo_coeff=None)

as_scanner()

Generating a scanner/solver for MP2 PES.

The returned solver is a function. This function requires one argument “mol” as input and returns total MP2 energy.

The solver will automatically use the results of last calculation as the initial guess of the new calculation. All parameters assigned in the MP2 and the underlying SCF objects (conv_tol, max_memory etc) are automatically applied in the solver.

Note scanner has side effects. It may change many underlying objects (_scf, with_df, with_x2c, …) during calculation.

Examples:

>>> from pyscf import gto, scf, mp
>>> mol = gto.M(atom='H 0 0 0; F 0 0 1')
>>> mp2_scanner = mp.MP2(scf.RHF(mol)).as_scanner()
>>> e_tot = mp2_scanner(gto.M(atom='H 0 0 0; F 0 0 1.1'))
>>> e_tot = mp2_scanner(gto.M(atom='H 0 0 0; F 0 0 1.5'))

conv_tol = 1e-07

conv_tol_normt = 1e-05

density_fit(auxbasis=None, with_df=None)

dump_flags(verbose=None)

property e_tot

property emp2

energy(t2, eris)

MP2 energy

get_frozen_mask()

Get boolean mask for the restricted reference orbitals.

In the returned boolean (mask) array of frozen orbital indices, the element is False if it corresonds to the frozen orbital.

get_nmo()

get_nocc()

init_amps(mo_energy=None, mo_coeff=None, eris=None, with_t2=True)

kernel(mo_energy=None, mo_coeff=None, eris=None, with_t2=True)

Args:

with_t2bool

Whether to generate and hold t2 amplitudes in memory.

make_fno(thresh=1e-06, pct_occ=None, nvir_act=None, t2=None)

Frozen natural orbitals

Returns:

frozenlist or ndarray

List of orbitals to freeze

no_coeffndarray

Semicanonical NO coefficients in the AO basis

make_rdm1(t2=None, eris=None, ao_repr=False)

Spin-traced one-particle density matrix. The occupied-virtual orbital response is not included.

dm1[p,q] = <q_alpha^dagger p_alpha> + <q_beta^dagger p_beta>

The convention of 1-pdm is based on McWeeney’s book, Eq (5.4.20). The contraction between 1-particle Hamiltonian and rdm1 is E = einsum(‘pq,qp’, h1, rdm1)

Kwargs:

ao_reprboolean

Whether to transfrom 1-particle density matrix to AO representation.

make_rdm2(t2=None, eris=None, ao_repr=False)

Spin-traced two-particle density matrix in MO basis

dm2[p,q,r,s] = sum_{sigma,tau} <p_sigma^dagger r_tau^dagger s_tau q_sigma>

Note the contraction between ERIs (in Chemist’s notation) and rdm2 is E = einsum(‘pqrs,pqrs’, eri, rdm2)

max_cycle = 50

property nmo

property nocc

nuc_grad_method()

reset(mol=None)

update_amps(t2, eris)

Update non-canonical MP2 amplitudes

pyscf.mp.mp2.RMP2

alias of pyscf.mp.mp2.MP2

pyscf.mp.mp2.as_scanner(mp)

Generating a scanner/solver for MP2 PES.

The returned solver is a function. This function requires one argument “mol” as input and returns total MP2 energy.

The solver will automatically use the results of last calculation as the initial guess of the new calculation. All parameters assigned in the MP2 and the underlying SCF objects (conv_tol, max_memory etc) are automatically applied in the solver.

Note scanner has side effects. It may change many underlying objects (_scf, with_df, with_x2c, …) during calculation.

Examples:

>>> from pyscf import gto, scf, mp
>>> mol = gto.M(atom='H 0 0 0; F 0 0 1')
>>> mp2_scanner = mp.MP2(scf.RHF(mol)).as_scanner()
>>> e_tot = mp2_scanner(gto.M(atom='H 0 0 0; F 0 0 1.1'))
>>> e_tot = mp2_scanner(gto.M(atom='H 0 0 0; F 0 0 1.5'))

pyscf.mp.mp2.energy(mp, t2, eris)

MP2 energy

pyscf.mp.mp2.get_frozen_mask(mp)

Get boolean mask for the restricted reference orbitals.

In the returned boolean (mask) array of frozen orbital indices, the element is False if it corresonds to the frozen orbital.

pyscf.mp.mp2.get_nmo(mp)

pyscf.mp.mp2.get_nocc(mp)

pyscf.mp.mp2.kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=True, verbose=None)

pyscf.mp.mp2.make_fno(mp, thresh=1e-06, pct_occ=None, nvir_act=None, t2=None)

Frozen natural orbitals

Returns:

frozenlist or ndarray

List of orbitals to freeze

no_coeffndarray

Semicanonical NO coefficients in the AO basis

pyscf.mp.mp2.make_rdm1(mp, t2=None, eris=None, ao_repr=False)

Spin-traced one-particle density matrix. The occupied-virtual orbital response is not included.

dm1[p,q] = <q_alpha^dagger p_alpha> + <q_beta^dagger p_beta>

The convention of 1-pdm is based on McWeeney’s book, Eq (5.4.20). The contraction between 1-particle Hamiltonian and rdm1 is E = einsum(‘pq,qp’, h1, rdm1)

Kwargs:

ao_reprboolean

Whether to transfrom 1-particle density matrix to AO representation.

pyscf.mp.mp2.make_rdm2(mp, t2=None, eris=None, ao_repr=False)

Spin-traced two-particle density matrix in MO basis

dm2[p,q,r,s] = sum_{sigma,tau} <p_sigma^dagger r_tau^dagger s_tau q_sigma>

Note the contraction between ERIs (in Chemist’s notation) and rdm2 is E = einsum(‘pqrs,pqrs’, eri, rdm2)

pyscf.mp.mp2.update_amps(mp, t2, eris)

Update non-canonical MP2 amplitudes

pyscf.mp.mp2f12_slow module

MP2-F12 (In testing)

Refs: * JCC 32, 2492 (2011); DOI:10.1002/jcc.21825 * JCP 139, 084112 (2013); DOI:10.1063/1.4818753

With strong orthogonalization ansatz 2

pyscf.mp.mp2f12_slow.energy_f12(mf, auxmol, zeta)

pyscf.mp.mp2f12_slow.find_cabs(mol, auxmol, lindep=1e-08)

pyscf.mp.mp2f12_slow.trans(eri, mos)

pyscf.mp.ump2 module

UMP2 with spatial integals

pyscf.mp.ump2.MP2

alias of pyscf.mp.ump2.UMP2

class pyscf.mp.ump2.UMP2(mf, frozen=None, mo_coeff=None, mo_occ=None)

Bases: pyscf.mp.mp2.MP2

Gradients(*args, **kwargs)

ao2mo(mo_coeff=None)

energy(t2, eris)

MP2 energy

get_frozen_mask()

Get boolean mask for the unrestricted reference orbitals.

In the returned boolean (mask) array of frozen orbital indices, the element is False if it corresonds to the frozen orbital.

get_nmo()

get_nocc()

init_amps(mo_energy=None, mo_coeff=None, eris=None, with_t2=True)

make_fno(thresh=1e-06, pct_occ=None, t2=None, eris=None)

Frozen natural orbitals

Returns:

frozenlist or ndarray

Length-2 list of orbitals to freeze

no_coeffndarray

Length-2 list of semicanonical NO coefficients in the AO basis

make_rdm1(t2=None, ao_repr=False)

One-particle spin density matrices dm1a, dm1b in MO basis (the occupied-virtual blocks due to the orbital response contribution are not included).

dm1a[p,q] = <q_alpha^dagger p_alpha> dm1b[p,q] = <q_beta^dagger p_beta>

The convention of 1-pdm is based on McWeeney’s book, Eq (5.4.20).

make_rdm2(t2=None, ao_repr=False)

Two-particle spin density matrices dm2aa, dm2ab, dm2bb in MO basis

dm2aa[p,q,r,s] = <q_alpha^dagger s_alpha^dagger r_alpha p_alpha> dm2ab[p,q,r,s] = <q_alpha^dagger s_beta^dagger r_beta p_alpha> dm2bb[p,q,r,s] = <q_beta^dagger s_beta^dagger r_beta p_beta>

(p,q correspond to one particle and r,s correspond to another particle) Two-particle density matrix should be contracted to integrals with the pattern below to compute energy

E = numpy.einsum(‘pqrs,pqrs’, eri_aa, dm2_aa) E+= numpy.einsum(‘pqrs,pqrs’, eri_ab, dm2_ab) E+= numpy.einsum(‘pqrs,rspq’, eri_ba, dm2_ab) E+= numpy.einsum(‘pqrs,pqrs’, eri_bb, dm2_bb)

where eri_aa[p,q,r,s] = (p_alpha q_alpha | r_alpha s_alpha ) eri_ab[p,q,r,s] = ( p_alpha q_alpha | r_beta s_beta ) eri_ba[p,q,r,s] = ( p_beta q_beta | r_alpha s_alpha ) eri_bb[p,q,r,s] = ( p_beta q_beta | r_beta s_beta )

nuc_grad_method()

update_amps(t2, eris)

Update non-canonical MP2 amplitudes

pyscf.mp.ump2.energy(mp, t2, eris)

MP2 energy

pyscf.mp.ump2.get_frozen_mask(mp)

Get boolean mask for the unrestricted reference orbitals.

In the returned boolean (mask) array of frozen orbital indices, the element is False if it corresonds to the frozen orbital.

pyscf.mp.ump2.get_nmo(mp)

pyscf.mp.ump2.get_nocc(mp)

pyscf.mp.ump2.kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=True, verbose=None)

pyscf.mp.ump2.make_fno(mp, thresh=1e-06, pct_occ=None, t2=None, eris=None)

Frozen natural orbitals

Returns:

frozenlist or ndarray

Length-2 list of orbitals to freeze

no_coeffndarray

Length-2 list of semicanonical NO coefficients in the AO basis

pyscf.mp.ump2.make_rdm1(mp, t2=None, ao_repr=False)

One-particle spin density matrices dm1a, dm1b in MO basis (the occupied-virtual blocks due to the orbital response contribution are not included).

dm1a[p,q] = <q_alpha^dagger p_alpha> dm1b[p,q] = <q_beta^dagger p_beta>

The convention of 1-pdm is based on McWeeney’s book, Eq (5.4.20).

pyscf.mp.ump2.make_rdm2(mp, t2=None, ao_repr=False)

Two-particle spin density matrices dm2aa, dm2ab, dm2bb in MO basis

dm2aa[p,q,r,s] = <q_alpha^dagger s_alpha^dagger r_alpha p_alpha> dm2ab[p,q,r,s] = <q_alpha^dagger s_beta^dagger r_beta p_alpha> dm2bb[p,q,r,s] = <q_beta^dagger s_beta^dagger r_beta p_beta>

(p,q correspond to one particle and r,s correspond to another particle) Two-particle density matrix should be contracted to integrals with the pattern below to compute energy

E = numpy.einsum(‘pqrs,pqrs’, eri_aa, dm2_aa) E+= numpy.einsum(‘pqrs,pqrs’, eri_ab, dm2_ab) E+= numpy.einsum(‘pqrs,rspq’, eri_ba, dm2_ab) E+= numpy.einsum(‘pqrs,pqrs’, eri_bb, dm2_bb)

where eri_aa[p,q,r,s] = (p_alpha q_alpha | r_alpha s_alpha ) eri_ab[p,q,r,s] = ( p_alpha q_alpha | r_beta s_beta ) eri_ba[p,q,r,s] = ( p_beta q_beta | r_alpha s_alpha ) eri_bb[p,q,r,s] = ( p_beta q_beta | r_beta s_beta )

pyscf.mp.ump2.update_amps(mp, t2, eris)

Update non-canonical MP2 amplitudes

Module contents

Moller-Plesset perturbation theory

pyscf.mp.GMP2(mf, frozen=None, mo_coeff=None, mo_occ=None)

pyscf.mp.MP2(mf, frozen=None, mo_coeff=None, mo_occ=None)

restricted MP2 with canonical HF and non-canonical HF reference

Attributes:

verboseint

Print level. Default value equals to Mole.verbose

max_memoryfloat or int

Allowed memory in MB. Default value equals to Mole.max_memory

conv_tolfloat

For non-canonical MP2, converge threshold for MP2 correlation energy. Default value is 1e-7.

conv_tol_normtfloat

For non-canonical MP2, converge threshold for norm(t2). Default value is 1e-5.

max_cycleint

For non-canonical MP2, max number of MP2 iterations. Default value is 50.

diis_spaceint

For non-canonical MP2, DIIS space size in MP2 iterations. Default is 6.

level_shiftfloat

A shift on virtual orbital energies to stablize the MP2 iterations.

frozenint or list

If integer is given, the inner-most orbitals are excluded from MP2 amplitudes. Given the orbital indices (0-based) in a list, both occupied and virtual orbitals can be frozen in MP2 calculation.

>>> mol = gto.M(atom = 'H 0 0 0; F 0 0 1.1', basis = 'ccpvdz')
>>> mf = scf.RHF(mol).run()
>>> # freeze 2 core orbitals
>>> pt = mp.MP2(mf).set(frozen = 2).run()
>>> # freeze 2 core orbitals and 3 high lying unoccupied orbitals
>>> pt.set(frozen = [0,1,16,17,18]).run()

Saved results

e_corrfloat

MP2 correlation correction

e_totfloat

Total MP2 energy (HF + correlation)

t2 :

T amplitudes t2[i,j,a,b] (i,j in occ, a,b in virt)

pyscf.mp.RMP2(mf, frozen=None, mo_coeff=None, mo_occ=None)

restricted MP2 with canonical HF and non-canonical HF reference

Attributes:

verboseint

Print level. Default value equals to Mole.verbose

max_memoryfloat or int

Allowed memory in MB. Default value equals to Mole.max_memory

conv_tolfloat

For non-canonical MP2, converge threshold for MP2 correlation energy. Default value is 1e-7.

conv_tol_normtfloat

For non-canonical MP2, converge threshold for norm(t2). Default value is 1e-5.

max_cycleint

For non-canonical MP2, max number of MP2 iterations. Default value is 50.

diis_spaceint

For non-canonical MP2, DIIS space size in MP2 iterations. Default is 6.

level_shiftfloat

A shift on virtual orbital energies to stablize the MP2 iterations.

frozenint or list

If integer is given, the inner-most orbitals are excluded from MP2 amplitudes. Given the orbital indices (0-based) in a list, both occupied and virtual orbitals can be frozen in MP2 calculation.

>>> mol = gto.M(atom = 'H 0 0 0; F 0 0 1.1', basis = 'ccpvdz')
>>> mf = scf.RHF(mol).run()
>>> # freeze 2 core orbitals
>>> pt = mp.MP2(mf).set(frozen = 2).run()
>>> # freeze 2 core orbitals and 3 high lying unoccupied orbitals
>>> pt.set(frozen = [0,1,16,17,18]).run()

Saved results

e_corrfloat

MP2 correlation correction

e_totfloat

Total MP2 energy (HF + correlation)

t2 :

T amplitudes t2[i,j,a,b] (i,j in occ, a,b in virt)

pyscf.mp.UMP2(mf, frozen=None, mo_coeff=None, mo_occ=None)