#!/usr/bin/env python
# Copyright 2017-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Authors: James D. McClain
# Timothy Berkelbach <tim.berkelbach@gmail.com>
#
from functools import reduce
import numpy as np
import h5py
from pyscf import lib
from pyscf.lib import logger
from pyscf import __config__
from pyscf.pbc import scf
from pyscf.pbc.lib import kpts_helper
from pyscf.pbc.mp.kmp2 import (get_nocc, get_nmo, padding_k_idx,
padded_mo_coeff, get_frozen_mask)
from pyscf.pbc.df import df
from pyscf.pbc import tools
from pyscf.pbc.cc.ccsd import _adjust_occ
# einsum = np.einsum
einsum = lib.einsum
direct_sum = lib.direct_sum
[docs]
def kernel(cis, nroots=1, eris=None, kptlist=None, **kargs):
"""CIS excitation energy with k-point sampling.
Arguments:
cis {KCIS} -- A KCIS instance
Keyword Arguments:
nroots {int} -- Number of requested excitation energies (default: {1})
eris {_CIS_ERIS} -- Depending on cis.direct, eris may
contain 4-center (cis.direct=False) or 3-center (cis.direct=True)
electron repulsion integrals (default: {None})
kptlist {list} -- A list of indices for k-shift, i.e. the exciton momentum.
Available k-shift indices depend on the k-point mesh. For example,
a 2 by 2 by 2 k-point mesh allows at most 8 k-shift values, which can
be targeted by [0, 1, 2, 3, 4, 5, 6, 7]. When kptlist=None, all k-shift
will be computed. (default: {None})
Returns:
tuple -- A tuple of excitation energies and corresponding eigenvectors
"""
cpu0 = (logger.process_clock(), logger.perf_counter())
log = logger.Logger(cis.stdout, cis.verbose)
cis.dump_flags()
if eris is None:
eris = cis.ao2mo()
nkpts = cis.nkpts
nocc = cis.nocc
nvir = cis.nmo - nocc
dtype = eris.dtype
if kptlist is None:
kptlist = range(nkpts)
r_size = nkpts * nocc * nvir
nroots = min(nroots, r_size)
evals = [None] * len(kptlist)
evecs = [None] * len(kptlist)
cpu1 = (logger.process_clock(), logger.perf_counter())
for k, kshift in enumerate(kptlist):
print("\nkshift =", kshift)
if cis.davidson:
# Davidson diagonalization
matvec, diag = cis.gen_matvec(kshift, eris=eris)
if diag.size != r_size:
raise ValueError("Number of diagonal elements in H does not match r vector size")
guess = cis.get_init_guess(nroots, diag=diag)
def precond(r, e0, x0):
return r/(e0-diag+1e-12)
eig = lib.davidson_nosym1
conv, eigval, eigvec = eig(matvec, guess, precond, tol=cis.conv_tol,
max_cycle=cis.max_cycle, max_space=cis.max_space,
max_memory=cis.max_memory, nroots=nroots, verbose=cis.verbose)
else:
# Exact diagonalization
if not cis.build_full_H:
H = np.zeros([r_size, r_size], dtype=dtype)
for col in range(r_size):
vec = np.zeros(r_size, dtype=dtype)
vec[col] = 1.0
H[:, col] = cis_matvec_singlet(cis, vec, kshift, eris=eris)
else:
H = cis_H(cis, kshift, eris=eris)
eigval, eigvec = np.linalg.eig(H)
idx = eigval.argsort()[:nroots]
eigval = eigval[idx]
eigvec = eigvec[:, idx]
for n in range(nroots):
logger.info(cis, "CIS root %d E = %.16g", n, eigval[n])
evals[k] = eigval
evecs[k] = eigvec
log.timer("CIS diagonalization", *cpu1)
log.timer("CIS", *cpu0)
return evals, evecs
[docs]
def cis_matvec_singlet(cis, vector, kshift, eris=None):
"""Compute matrix-vector product of the Hamiltonion matrix and a CIS c
oefficient vector, in the space of single excitation.
Arguments:
cis {KCIS} -- A KCIS instance
vector {1D array} -- CIS coefficient vector
kshift {int} -- k-shift index. A k-shift vector is an exciton momentum.
Available k-shift indices depend on the k-point mesh. For example,
a 2 by 2 by 2 k-point mesh allows at most 8 k-shift values, which can
be targeted by 0, 1, 2, 3, 4, 5, 6, or 7.
Keyword Arguments:
eris {_CIS_ERIS} -- Depending on cis.direct, eris may
contain 4-center (cis.direct=False) or 3-center (cis.direct=True)
electron repulsion integrals (default: {None})
Returns:
1D array -- matrix-vector product of the Hamiltonion matrix and the
input vector.
"""
if eris is None:
eris = cis.ao2mo()
nkpts = cis.nkpts
nocc = cis.nocc
kconserv_r = cis.get_kconserv_r(kshift)
r = cis.vector_to_amplitudes(vector)
# Should use Fock diagonal elements to build (e_a - e_i) matrix
epsilons = [eris.fock[k].diagonal().real for k in range(nkpts)]
Hr = np.zeros_like(r)
for ki in range(nkpts):
ka = kconserv_r[ki]
Hr[ki] += einsum('ia,a->ia', r[ki], epsilons[ka][nocc:])
Hr[ki] -= einsum('ia,i->ia', r[ki], epsilons[ki][:nocc])
if not cis.direct:
for ki in range(nkpts):
ka = kconserv_r[ki]
# x: kj
Hr[ki] += 2.0 * einsum("xjb,xajib->ia", r, eris.voov[ka, :, ki])
Hr[ki] -= einsum("xjb,xjaib->ia", r, eris.ovov[:, ka, ki])
else:
for ki in range(nkpts):
ka = kconserv_r[ki]
for kj in range(nkpts):
kb = kconserv_r[kj]
# r_ia <- 2 r_jb (ai|jb) = 2 r_jb B^L_jb B^L_ai
L = 2.0 * einsum("jb,Ljb->L", r[kj], eris.Lpq_mo[kj,kb][:, :nocc, nocc:])
tmp = einsum("L,Lai->ia", L, eris.Lpq_mo[ka,ki][:, nocc:, :nocc])
# r_ia <- - r_jb (ab|ji) = -r_jb B^L_ab B^L_ji
Lja = -1.0 * einsum("jb,Lab->Lja", r[kj], eris.Lpq_mo[ka,kb][:, nocc:, nocc:])
tmp += einsum("Lja,Lji->ia", Lja, eris.Lpq_mo[kj,ki][:, :nocc, :nocc])
Hr[ki] += (1. / nkpts) * tmp
vector = cis.amplitudes_to_vector(Hr)
return vector
[docs]
def cis_H(cis, kshift, eris=None):
"""Build full Hamiltonian matrix in the space of single excitation,
i.e. CIS Hamiltonian.
Arguments:
cis {KCIS} -- A KCIS instance
kshift {int} -- k-shift index. A k-shift vector is an exciton momentum.
Available k-shift indices depend on the k-point mesh. For example,
a 2 by 2 by 2 k-point mesh allows at most 8 k-shift values, which can
be targeted by 0, 1, 2, 3, 4, 5, 6, or 7.
Keyword Arguments:
eris {_CIS_ERIS} -- Depending on cis.direct, eris may
contain 4-center (cis.direct=False) or 3-center (cis.direct=True)
electron repulsion integrals (default: {None})
Raises:
MemoryError: MemoryError will be raise if there is not enough space to
store the full Hamiltonian matrix, which scales as Nk^2 O^2 V^2
Returns:
2D array -- the Hamiltonian matrix reshaped into (ki,i,a) by (kj,j,b)
"""
cpu0 = (logger.process_clock(), logger.perf_counter())
log = logger.Logger(cis.stdout, cis.verbose)
if eris is None:
eris = cis.ao2mo()
nkpts = cis.nkpts
nocc = cis.nocc
nmo = cis.nmo
nvir = nmo - nocc
nov = nocc * nvir
r_size = nkpts * nov
memory_needed = (r_size ** 2) * 16 / 1e6
memory_now = lib.current_memory()[0]
if memory_needed + memory_now >= cis.max_memory:
raise MemoryError("Not enough memory to store full CIS Hamiltonian")
kconserv_r = cis.get_kconserv_r(kshift)
dtype = eris.dtype
epsilons = [eris.fock[k].diagonal().real for k in range(nkpts)]
H = np.zeros((nkpts, nkpts, nov, nov), dtype=dtype)
# <ia|H|jb> <- (esp_a - esp_i) \delta{i,j} \delta{a,b}
for ki in range(nkpts):
ka = kconserv_r[ki]
diag_ia = direct_sum("a-i->ia", epsilons[ka][nocc:], epsilons[ki][:nocc])
diag_ia = np.ravel(diag_ia)
np.fill_diagonal(H[ki, ki], diag_ia)
# <ia|H|jb> <- 2<ja|bi> - <ja|ib>
if not cis.direct:
for ki in range(nkpts):
ka = kconserv_r[ki]
for kj in range(nkpts):
kb = kconserv_r[kj]
# contribution from 2 <ja|bi> = 2 <aj|ib>
tmp = 2. * eris.voov[ka, kj, ki].transpose(2,0,1,3)
# contribution from -<ja|ib>
tmp -= eris.ovov[kj, ka, ki].transpose(2,1,0,3)
H[ki, kj] += tmp.reshape(nov, nov)
else:
for ki in range(nkpts):
ka = kconserv_r[ki]
for kj in range(nkpts):
kb = kconserv_r[kj]
# contribution from 2 (ai|jb) = 2 B^L_ai B^L_jb
tmp = 2. * einsum("Lai,Ljb->iajb",
eris.Lpq_mo[ka,ki][:, nocc:, :nocc],
eris.Lpq_mo[kj,kb][:, :nocc, nocc:])
# contribution from -(ab|ji) = - B^L_ab B^L_ji
tmp -= einsum("Lab,Lji->iajb",
eris.Lpq_mo[ka,kb][:, nocc:, nocc:],
eris.Lpq_mo[kj,ki][:, :nocc, :nocc])
tmp *= 1. / nkpts
H[ki, kj] += tmp.reshape(nov, nov)
H = H.reshape(nkpts, nkpts, nocc, nvir, nocc, nvir).transpose(0,2,3,1,4,5).reshape(r_size, r_size)
log.timer("build full CIS Hamiltonian", *cpu0)
return H
[docs]
def cis_diag(cis, kshift, eris=None):
"""Diagonal elements of CIS Hamiltonian.
Arguments:
cis {KCIS} -- A KCIS instance
kshift {int} -- k-shift index. A k-shift vector is an exciton momentum.
Available k-shift indices depend on the k-point mesh. For example,
a 2 by 2 by 2 k-point mesh allows at most 8 k-shift values, which can
be targeted by 0, 1, 2, 3, 4, 5, 6, or 7.
Keyword Arguments:
eris {_CIS_ERIS} -- Depending on cis.direct, eris may
contain 4-center (cis.direct=False) or 3-center (cis.direct=True)
electron repulsion integrals (default: {None})
Returns:
1D array -- an array formed by diagonal elements of CIS Hamiltonian
"""
if eris is None:
eris = cis.ao2mo()
nkpts = cis.nkpts
nocc = cis.nocc
nmo = cis.nmo
nvir = nmo - nocc
kconserv_r = cis.get_kconserv_r(kshift)
dtype = eris.dtype
epsilons = [eris.fock[k].diagonal().real for k in range(nkpts)]
Hdiag = np.zeros((nkpts, nocc, nvir), dtype=dtype)
for ki in range(nkpts):
ka = kconserv_r[ki]
Hdiag[ki] = direct_sum("a-i->ia", epsilons[ka][nocc:], epsilons[ki][:nocc])
if not cis.direct:
for ki in range(nkpts):
ka = kconserv_r[ki]
Hdiag[ki] += 2. * einsum("aiia->ia", eris.voov[ka, ki, ki])
Hdiag[ki] -= einsum("iaia->ia", eris.ovov[ki, ka, ki])
else:
for ki in range(nkpts):
ka = kconserv_r[ki]
tmp = 2. * einsum("Lai,Lia->ia", eris.Lpq_mo[ka, ki][:, nocc:, :nocc], eris.Lpq_mo[ki,ka][:, :nocc, nocc:])
tmp -= einsum("Laa,Lii->ia", eris.Lpq_mo[ka, ka][:, nocc:, nocc:], eris.Lpq_mo[ki, ki][:, :nocc, :nocc])
Hdiag[ki] += (1. / nkpts) * tmp
return np.ravel(Hdiag)
[docs]
class KCIS(lib.StreamObject):
def __init__(self, mf, frozen=None, mo_coeff=None, mo_occ=None):
assert isinstance(mf, scf.khf.KSCF)
if mo_coeff is None:
mo_coeff = mf.mo_coeff
if mo_occ is None:
mo_occ = mf.mo_occ
self._scf = mf
self.kpts = mf.kpts
self.verbose = mf.verbose
self.max_memory = mf.max_memory
self.max_space = getattr(__config__, 'kcis_rhf_max_space', 20)
self.max_cycle = getattr(__config__, 'kcis_rhf_max_cycle', 50)
self.conv_tol = getattr(__config__, 'kcis_rhf_conv_tol', 1e-7)
##################################################
# don't modify the following attributes, unless you know what you are doing
self.keep_exxdiv = False
self.direct = False
self.build_full_H = False
self.davidson = True
self.khelper = kpts_helper.KptsHelper(mf.cell, mf.kpts)
self.mo_coeff = mo_coeff
self.mo_occ = mo_occ
self.frozen = frozen
self._nocc = None
self._nmo = None
self.voov = None
self.ovov = None
[docs]
def dump_flags(self, verbose=None):
log = logger.new_logger(self, verbose)
log.info("")
log.info("******** %s ********", self.__class__)
log.info("nkpts = %d", self.nkpts)
log.info("CIS nocc = %d, nmo = %d", self.nocc, self.nmo)
if self.frozen is not None:
log.info("frozen orbitals = %s", self.frozen)
log.info("max_memory %d MB (current use %d MB)",
self.max_memory, lib.current_memory()[0])
if self.direct:
log.info("cis.direct = True; voov and ovov will not be computed")
return self
@property
def nkpts(self):
return len(self.kpts)
@property
def nocc(self):
return self.get_nocc()
@property
def nmo(self):
return self.get_nmo()
get_nocc = get_nocc
get_nmo = get_nmo
get_frozen_mask = get_frozen_mask
get_diag = cis_diag
matvec = cis_matvec_singlet
kernel = kernel
[docs]
def vector_size(self):
nocc = self.nocc
nvir = self.nmo - nocc
nkpts = self.nkpts
return nkpts * nocc * nvir
[docs]
def vector_to_amplitudes(self, vector, nkpts=None, nmo=None, nocc=None):
if nmo is None:
nmo = self.nmo
if nocc is None:
nocc = self.nocc
if nkpts is None:
nkpts = self.nkpts
nvir = nmo - nocc
return vector[: nkpts * nocc * nvir].copy().reshape(nkpts, nocc, nvir)
[docs]
def amplitudes_to_vector(self, r):
return r.ravel()
[docs]
def ao2mo(self, mo_coeff=None):
return _CIS_ERIS(self, mo_coeff)
[docs]
def gen_matvec(self, kshift, eris=None, **kwargs):
if eris is None:
eris = self.ao2mo()
diag = self.get_diag(kshift, eris)
matvec = lambda xs: [self.matvec(x, kshift, eris) for x in xs]
return matvec, diag
[docs]
def get_init_guess(self, nroots=1, diag=None):
idx = diag.argsort()
size = self.vector_size()
dtype = getattr(diag, 'dtype', self.mo_coeff[0].dtype)
nroots = min(nroots, size)
guess = []
for i in idx[:nroots]:
g = np.zeros(size, dtype)
g[i] = 1.0
guess.append(g)
return guess
[docs]
def get_kconserv_r(self, kshift):
r"""Get the momentum conservation array for a set of k-points.
Given k-point index m the array kconserv_r1[m] returns the index n that
satisfies momentum conservation,
(k(m) - k(n) - kshift) \dot a = 2n\pi
This is used for symmetry of 1p-1h excitation operator vector
R_{m k_m}^{n k_n} is zero unless n satisfies the above.
Note that this method is adapted from `kpts_helper.get_kconserv()`.
Arguments:
kshift {int} -- index of momentum vector. It can be chosen as any of the available
k-point index based on the specified kpt mesh.
E.g. int from 0 to 7 can be chosen for a [2,2,2] grid.
Returns:
list -- a list of k(n) corresponding to k(m) that ranges from 0 to max_k_index
"""
kconserv = self.khelper.kconserv
kconserv_r = kconserv[:, kshift, 0].copy()
return kconserv_r
# TODO Merge this with kccsd_rhf._ERIS, which contains more ints (e.g. oooo,
# ooov, etc.) than we need here
class _CIS_ERIS:
def __init__(self, cis, mo_coeff=None, method="incore"):
log = logger.Logger(cis.stdout, cis.verbose)
cput0 = (logger.process_clock(), logger.perf_counter())
cell = cis._scf.cell
nocc = cis.nocc
nmo = cis.nmo
nvir = nmo - nocc
nkpts = cis.nkpts
kpts = cis.kpts
if mo_coeff is None:
mo_coeff = cis.mo_coeff
dtype = mo_coeff[0].dtype
mo_coeff = self.mo_coeff = padded_mo_coeff(cis, mo_coeff)
# Re-make our fock MO matrix elements from density and fock AO
dm = cis._scf.make_rdm1(cis.mo_coeff, cis.mo_occ)
exxdiv = cis._scf.exxdiv if cis.keep_exxdiv else None
with lib.temporary_env(cis._scf, exxdiv=exxdiv):
# _scf.exxdiv affects eris.fock. HF exchange correction should be
# excluded from the Fock matrix.
fockao = cis._scf.get_hcore() + cis._scf.get_veff(cell, dm)
self.fock = np.asarray([reduce(np.dot, (mo.T.conj(), fockao[k], mo))
for k, mo in enumerate(mo_coeff)])
self.mo_energy = [self.fock[k].diagonal().real for k in range(nkpts)]
if not cis.keep_exxdiv:
# Add HFX correction in the self.mo_energy to improve convergence in
# CCSD iteration. It is useful for the 2D systems since their occupied and
# the virtual orbital energies may overlap which may lead to numerical
# issue in the CCSD iterations.
# FIXME: Whether to add this correction for other exxdiv treatments?
# Without the correction, MP2 energy may be largely off the correct value.
madelung = tools.madelung(cell, kpts)
self.mo_energy = [
_adjust_occ(mo_e, nocc, -madelung) for k, mo_e in enumerate(self.mo_energy)
]
# Get location of padded elements in occupied and virtual space.
nocc_per_kpt = get_nocc(cis, per_kpoint=True)
nonzero_padding = padding_k_idx(cis, kind="joint")
# Check direct and indirect gaps for possible issues with CCSD convergence.
mo_e = [self.mo_energy[kp][nonzero_padding[kp]] for kp in range(nkpts)]
mo_e = np.sort([y for x in mo_e for y in x]) # Sort de-nested array
gap = mo_e[np.sum(nocc_per_kpt)] - mo_e[np.sum(nocc_per_kpt) - 1]
if gap < 1e-5:
logger.warn(
cis,
"HOMO-LUMO gap %s too small for KCCSD. "
"May cause issues in convergence.",
gap,
)
memory_needed = (nkpts ** 3 * nocc ** 2 * nvir ** 2) * 16 / 1e6
# CIS only needs two terms: <aj|ib> and <aj|bi>; another factor of two for safety
memory_needed *= 4
memory_now = lib.current_memory()[0]
fao2mo = cis._scf.with_df.ao2mo
kconserv = cis.khelper.kconserv
khelper = cis.khelper
if cis.direct and type(cis._scf.with_df) is not df.GDF:
raise ValueError("CIS direct method must be used with GDF")
if (cis.direct and type(cis._scf.with_df) is df.GDF
and cell.dimension != 2):
# cis._scf.with_df needs to be df.GDF only (not MDF)
_init_cis_df_eris(cis, self)
else:
if (
method == "incore"
and (memory_needed + memory_now < cis.max_memory)
or cell.incore_anyway
):
log.info("using incore ERI storage")
self.ovov = np.empty(
(nkpts, nkpts, nkpts, nocc, nvir, nocc, nvir), dtype=dtype
)
self.voov = np.empty(
(nkpts, nkpts, nkpts, nvir, nocc, nocc, nvir), dtype=dtype
)
for (ikp, ikq, ikr) in khelper.symm_map.keys():
iks = kconserv[ikp, ikq, ikr]
eri_kpt = fao2mo(
(mo_coeff[ikp], mo_coeff[ikq], mo_coeff[ikr], mo_coeff[iks]),
(kpts[ikp], kpts[ikq], kpts[ikr], kpts[iks]),
compact=False,
)
if dtype == np.double:
eri_kpt = eri_kpt.real
eri_kpt = eri_kpt.reshape(nmo, nmo, nmo, nmo)
for (kp, kq, kr) in khelper.symm_map[(ikp, ikq, ikr)]:
eri_kpt_symm = khelper.transform_symm(
eri_kpt, kp, kq, kr
).transpose(0, 2, 1, 3)
self.ovov[kp, kr, kq] = (
eri_kpt_symm[:nocc, nocc:, :nocc, nocc:] / nkpts
)
self.voov[kp, kr, kq] = (
eri_kpt_symm[nocc:, :nocc, :nocc, nocc:] / nkpts
)
self.dtype = dtype
else:
log.info("using HDF5 ERI storage")
self.feri1 = lib.H5TmpFile()
self.ovov = self.feri1.create_dataset(
"ovov", (nkpts, nkpts, nkpts, nocc, nvir, nocc, nvir), dtype.char
)
self.voov = self.feri1.create_dataset(
"voov", (nkpts, nkpts, nkpts, nvir, nocc, nocc, nvir), dtype.char
)
# <ia|pq> = (ip|aq)
cput1 = logger.process_clock(), logger.perf_counter()
for kp in range(nkpts):
for kq in range(nkpts):
for kr in range(nkpts):
ks = kconserv[kp, kq, kr]
orbo_p = mo_coeff[kp][:, :nocc]
orbv_r = mo_coeff[kr][:, nocc:]
buf_kpt = fao2mo(
(orbo_p, mo_coeff[kq], orbv_r, mo_coeff[ks]),
(kpts[kp], kpts[kq], kpts[kr], kpts[ks]),
compact=False,
)
if mo_coeff[0].dtype == np.double:
buf_kpt = buf_kpt.real
buf_kpt = buf_kpt.reshape(nocc, nmo, nvir, nmo).transpose(
0, 2, 1, 3
)
self.dtype = buf_kpt.dtype
self.ovov[kp, kr, kq, :, :, :, :] = (
buf_kpt[:, :, :nocc, nocc:] / nkpts
)
self.voov[kr, kp, ks, :, :, :, :] = (
buf_kpt[:, :, nocc:, :nocc].transpose(1, 0, 3, 2) / nkpts
)
cput1 = log.timer_debug1("transforming ovpq", *cput1)
log.timer("CIS integral transformation", *cput0)
def _init_cis_df_eris(cis, eris):
"""Add 3-center electron repulsion integrals, i.e. (L|pq), in `eris`,
where `L` denotes DF auxiliary basis functions and `p` and `q` canonical
crystalline orbitals. Note that `p` and `q` contain kpt indices `kp` and `kq`,
and the third kpt index `kL` is determined by the conservation of momentum.
Arguments:
cis {KCIS} -- A KCIS instance
eris {_CIS_ERIS} -- A _CIS_ERIS instance to which we want to add 3c ints
Returns:
_CIS_ERIS -- A _CIS_ERIS instance with 3c ints
"""
from pyscf.ao2mo import _ao2mo
from pyscf.pbc.lib.kpts_helper import gamma_point
log = logger.Logger(cis.stdout, cis.verbose)
if cis._scf.with_df._cderi is None:
cis._scf.with_df.build()
cell = cis._scf.cell
if cell.dimension == 2:
# 2D ERIs are not positive definite. The 3-index tensors are stored in
# two part. One corresponds to the positive part and one corresponds
# to the negative part. The negative part is not considered in the
# DF-driven CCSD implementation.
raise NotImplementedError
nmo = cis.nmo
nao = cell.nao_nr()
kpts = cis.kpts
nkpts = len(kpts)
if gamma_point(kpts):
dtype = np.double
else:
dtype = np.complex128
eris.dtype = dtype = np.result_type(dtype, *eris.mo_coeff)
eris.Lpq_mo = Lpq_mo = np.empty((nkpts, nkpts), dtype=object)
cput0 = (logger.process_clock(), logger.perf_counter())
with df.CDERIArray(cis._scf.with_df._cderi) as cderi_array:
tao = []
ao_loc = None
for ki in range(nkpts):
for kj in range(nkpts):
Lpq_ao = cderi_array[ki,kj]
mo = np.hstack((eris.mo_coeff[ki], eris.mo_coeff[kj]))
mo = np.asarray(mo, dtype=dtype, order='F')
if dtype == np.double:
out = _ao2mo.nr_e2(Lpq_ao, mo, (0, nmo, nmo, nmo+nmo), aosym='s2')
else:
#Note: Lpq.shape[0] != naux if linear dependency is found in auxbasis
if Lpq_ao[0].size != nao**2: # aosym = 's2'
Lpq_ao = lib.unpack_tril(Lpq_ao).astype(np.complex128)
out = _ao2mo.r_e2(Lpq_ao, mo, (0, nmo, nmo, nmo+nmo), tao, ao_loc)
Lpq_mo[ki, kj] = out.reshape(-1, nmo, nmo)
log.timer_debug1("transforming DF-CIS integrals", *cput0)
return eris
if __name__ == "__main__":
from pyscf.pbc import gto, ci
cell = gto.Cell()
cell.atom = """
C 0.000000000000 0.000000000000 0.000000000000
C 1.685068664391 1.685068664391 1.685068664391
"""
cell.basis = "gth-szv"
cell.pseudo = "gth-pade"
cell.a = """
0.000000000, 3.370137329, 3.370137329
3.370137329, 0.000000000, 3.370137329
3.370137329, 3.370137329, 0.000000000"""
cell.unit = "B"
cell.verbose = 7
cell.build()
# Running HF and MP2 with 1x1x2 Monkhorst-Pack k-point mesh
kmf = scf.KRHF(cell, kpts=cell.make_kpts([1, 1, 2]), exxdiv=None)
ehf = kmf.kernel()
mycis = ci.KCIS(kmf)
e_cis, v_cis = mycis.kernel(nroots=1, kptlist=[0])
print(e_cis[0] - 0.2239201285373249)