def _make_shared_1e(self):
cput0 = (time.clock(), time.time())
log = Logger(self.stdout, self.verbose)
t1, t2, eris = self.t1, self.t2, self.eris
self.Loo = imd.Loo(t1, t2, eris)
self.Lvv = imd.Lvv(t1, t2, eris)
self.Fov = imd.cc_Fov(t1, t2, eris)
log.timer('EOM-CCSD shared one-electron intermediates', *cput0)
def _make_shared_2e(self):
cput0 = (time.clock(), time.time())
log = Logger(self.stdout, self.verbose)
t1, t2, eris = self.t1, self.t2, self.eris
# 2 virtuals
self.Wovov = imd.Wovov(t1, t2, eris)
self.Wovvo = imd.Wovvo(t1, t2, eris)
self.Woovv = eris.ovov.transpose(0, 2, 1, 3)
log.timer('EOM-CCSD shared two-electron intermediates', *cput0)
def energy(cc, t1, t2, eris):
log = Logger(cc.stdout, cc.verbose)
nkpts = len(cc.kpts)
e = 2 * lib.einsum('ia,ia', eris.fov, t1)
tau = lib.einsum('ia,jb->ijab', t1, t1)
tau += t2
e += 2 * lib.einsum('ijab,iajb', tau, eris.ovov)
e += -lib.einsum('ijab,ibja', tau, eris.ovov)
if abs(e.imag) > 1e-4:
log.warn('Non-zero imaginary part found in KRCCSD energy %s', e)
return e.real / nkpts
def make_ip(self, partition=None):
self._make_shared_1e()
if self._made_shared_2e is False and partition != 'mp':
self._make_shared_2e()
self._made_shared_2e = True
cput0 = (time.clock(), time.time())
log = Logger(self.stdout, self.verbose)
t1, t2, eris = self.t1, self.t2, self.eris
# 0 or 1 virtuals
if partition != 'mp':
self.Woooo = imd.Woooo(t1, t2, eris)
self.Wooov = imd.Wooov(t1, t2, eris)
self.Wovoo = imd.Wovoo(t1, t2, eris)
self.made_ip_imds = True
log.timer('EOM-CCSD IP intermediates', *cput0)
def make_ea(self, partition=None):
self._make_shared_1e()
if self._made_shared_2e is False and partition != 'mp':
self._make_shared_2e()
self._made_shared_2e = True
cput0 = (time.clock(), time.time())
log = Logger(self.stdout, self.verbose)
t1, t2, eris = self.t1, self.t2, self.eris
# 3 or 4 virtuals
self.Wvovv = imd.Wvovv(t1, t2, eris)
if partition == 'mp':
self.Wvvvo = imd.Wvvvo(t1, t2, eris)
else:
self.Wvvvv = imd.Wvvvv(t1, t2, eris)
self.Wvvvo = imd.Wvvvo(t1, t2, eris, self.Wvvvv)
self.made_ea_imds = True
log.timer('EOM-CCSD EA intermediates', *cput0)
def kernel(eom,
nroots=1,
koopmans=True,
guess=None,
left=False,
eris=None,
imds=None,
partition=None,
kptlist=None,
dtype=None,
**kwargs):
cput0 = (time.clock(), time.time())
log = Logger(eom.stdout, eom.verbose)
eom.dump_flags()
if imds is None:
imds = eom.make_imds(eris)
size = eom.vector_size()
nroots = min(nroots, size)
from pyscf.pbc.lib.linalg_helper import eigs
matvec, diag = eom.gen_matvec(imds, left=left, **kwargs)
user_guess = False
if guess:
user_guess = True
assert len(guess) == nroots
for g in guess:
assert g.size == size
else:
user_guess = False
guess = eom.get_init_guess(nroots, koopmans, diag)
conv, evals, evecs = eigs(matvec,
size,
nroots,
x0=guess,
Adiag=diag,
verbose=eom.verbose)
evals = evals.real
for n, en, vn in zip(range(nroots), evals, evecs.T):
r1, r2 = eom.vector_to_amplitudes(vn)
qp_weight = r1.norm()**2
log.info('EOM-CCSD root %d E = %.16g qpwt = %0.6g', n, en, qp_weight)
log.timer('EOM-CCSD', *cput0)
return conv, evals, evecs
def init_amps(self, eris):
time0 = time.clock(), time.time()
log = Logger(self.stdout, self.verbose)
nocc = self.nocc
nvir = self.nmo - nocc
kpts = self.kpts
nkpts = self.nkpts
gvec = self._scf.cell.reciprocal_vectors()
sym1 = ['+-', [
kpts,
] * 2, None, gvec]
t1 = lib.zeros([nocc, nvir], eris.dtype, sym1)
t2 = eris.ovov.transpose(0, 2, 1, 3).conj() / eris.eijab
self.emp2 = 2 * lib.einsum('ijab,iajb', t2, eris.ovov)
self.emp2 -= lib.einsum('ijab,ibja', t2, eris.ovov)
self.emp2 = self.emp2.real / nkpts
log.info('Init t2, MP2 energy (with fock eigenvalue shift) = %.15g',
self.emp2)
log.timer('init mp2', *time0)
return self.emp2, t1, t2
def kernel(eom,
nroots=1,
koopmans=True,
guess=None,
left=False,
eris=None,
imds=None,
partition=None,
kptlist=None,
dtype=None,
**kwargs):
cput0 = (time.clock(), time.time())
eom.dump_flags()
log = Logger(eom.stdout, eom.verbose)
if imds is None:
imds = eom.make_imds(eris)
size = eom.vector_size()
nroots = min(nroots, size)
nkpts = eom.nkpts
if kptlist is None:
kptlist = range(nkpts)
if dtype is None:
dtype = imds.t1.dtype
evals = np.zeros((len(kptlist), nroots), np.float)
evecs = []
convs = np.zeros((len(kptlist), nroots), dtype)
from pyscf.pbc.lib.linalg_helper import eigs
for k, kshift in enumerate(kptlist):
matvec, diag = eom.gen_matvec(kshift, imds, left=left, **kwargs)
eom.update_symlib(kshift)
user_guess = False
if guess:
user_guess = True
assert len(guess) == nroots
for g in guess:
assert g.size == size
else:
user_guess = False
guess = eom.get_init_guess(kshift, nroots, koopmans, diag)
conv_k, evals_k, evecs_k = eigs(matvec,
size,
nroots,
x0=guess,
Adiag=diag,
verbose=eom.verbose)
evals_k = evals_k.real
evals[k] = evals_k.real
evecs.append(evecs_k)
convs[k] = conv_k
for n, en, vn in zip(range(nroots), evals_k, evecs_k.T):
r1, r2 = eom.vector_to_amplitudes(vn, kshift)
qp_weight = r1.norm()**2
log.info('EOM-CCSD root %d E = %.16g qpwt = %0.6g', n, en,
qp_weight)
log.timer('EOM-CCSD', *cput0)
evecs = np.vstack(tuple(evecs))
return convs, evals, evecs
def __init__(self, cc, mo_coeff=None):
from pyscf.pbc.cc.ccsd import _adjust_occ
import pyscf.pbc.tools.pbc as tools
if mo_coeff is None:
mo_coeff = cc.mo_coeff
cput0 = (time.clock(), time.time())
log = Logger(cc.stdout, cc.verbose)
self.lib = lib
nocc, nmo, nkpts = cc.nocc, cc.nmo, cc.nkpts
nvir = nmo - nocc
cell, kpts = cc._scf.cell, cc.kpts
gvec = cell.reciprocal_vectors()
sym1 = ['+-', [
kpts,
] * 2, None, gvec]
sym2 = ['+-+-', [
kpts,
] * 4, None, gvec]
mo_coeff = self.mo_coeff = padded_mo_coeff(cc, mo_coeff)
nonzero_opadding, nonzero_vpadding = padding_k_idx(cc, kind="split")
madelung = tools.madelung(cell, kpts)
dm = cc._scf.make_rdm1(cc.mo_coeff, cc.mo_occ)
with pyscflib.temporary_env(cc._scf, exxdiv=None):
fockao = cc._scf.get_hcore() + cc._scf.get_veff(cell, dm)
fock = np.asarray([
reduce(np.dot, (mo.T.conj(), fockao[k], mo))
for k, mo in enumerate(mo_coeff)
])
self.dtype = dtype = np.result_type(*fock).char
self.foo = tensor(fock[:, :nocc, :nocc], sym1)
self.fov = tensor(fock[:, :nocc, nocc:], sym1)
self.fvv = tensor(fock[:, nocc:, nocc:], sym1)
mo_energy = [fock[k].diagonal().real for k in range(nkpts)]
mo_energy = [
_adjust_occ(mo_e, nocc, -madelung)
for k, mo_e in enumerate(mo_energy)
]
mo_e_o = [e[:nocc] for e in mo_energy]
mo_e_v = [e[nocc:] + cc.level_shift for e in mo_energy]
foo_ = np.asarray([np.diag(e) for e in mo_e_o])
fvv_ = np.asarray([np.diag(e) for e in mo_e_v])
self._foo = tensor(foo_, sym1)
self._fvv = tensor(fvv_, sym1)
eia = np.zeros([nkpts, nocc, nvir])
for ki in range(nkpts):
eia[ki] = _get_epq([0, nocc, ki, mo_e_o, nonzero_opadding],
[0, nvir, ki, mo_e_v, nonzero_vpadding],
fac=[1.0, -1.0])
self.eia = tensor(eia, sym1)
self.oooo = zeros([nocc, nocc, nocc, nocc], dtype, sym2)
self.ooov = zeros([nocc, nocc, nocc, nvir], dtype, sym2)
self.ovov = zeros([nocc, nvir, nocc, nvir], dtype, sym2)
self.oovv = zeros([nocc, nocc, nvir, nvir], dtype, sym2)
self.ovvo = zeros([nocc, nvir, nvir, nocc], dtype, sym2)
self.ovvv = zeros([nocc, nvir, nvir, nvir], dtype, sym2)
self.vvvv = zeros([nvir, nvir, nvir, nvir], dtype, sym2)
self.eijab = zeros([nocc, nocc, nvir, nvir], np.float64, sym2)
with_df = cc._scf.with_df
fao2mo = cc._scf.with_df.ao2mo
kconserv = cc.khelper.kconserv
khelper = cc.khelper
jobs = list(khelper.symm_map.keys())
for itask in jobs:
ikp, ikq, ikr = itask
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.float: eri_kpt = eri_kpt.real
eri_kpt = eri_kpt.reshape(nmo, nmo, nmo, nmo) / nkpts
done = np.zeros([nkpts, nkpts, nkpts])
for (kp, kq, kr) in khelper.symm_map[(ikp, ikq, ikr)]:
if done[kp, kq, kr]: continue
eri_kpt_symm = khelper.transform_symm(eri_kpt, kp, kq, kr)
oooo = eri_kpt_symm[:nocc, :nocc, :nocc, :nocc]
ooov = eri_kpt_symm[:nocc, :nocc, :nocc, nocc:]
ovov = eri_kpt_symm[:nocc, nocc:, :nocc, nocc:]
oovv = eri_kpt_symm[:nocc, :nocc, nocc:, nocc:]
ovvo = eri_kpt_symm[:nocc, nocc:, nocc:, :nocc]
ovvv = eri_kpt_symm[:nocc, nocc:, nocc:, nocc:]
vvvv = eri_kpt_symm[nocc:, nocc:, nocc:, nocc:]
ks = kconserv[kp, kq, kr]
eia = _get_epq([0, nocc, kp, mo_e_o, nonzero_opadding],
[0, nvir, kq, mo_e_v, nonzero_vpadding],
fac=[1.0, -1.0])
ejb = _get_epq([0, nocc, kr, mo_e_o, nonzero_opadding],
[0, nvir, ks, mo_e_v, nonzero_vpadding],
fac=[1.0, -1.0])
eijab = eia[:, None, :, None] + ejb[None, :, None, :]
self.oooo.array[kp, kq, kr] = oooo
self.ooov.array[kp, kq, kr] = ooov
self.ovov.array[kp, kq, kr] = ovov
self.oovv.array[kp, kq, kr] = oovv
self.ovvo.array[kp, kq, kr] = ovvo
self.ovvv.array[kp, kq, kr] = ovvv
self.vvvv.array[kp, kq, kr] = vvvv
self.eijab.array[kp, kr, kq] = eijab
done[kp, kq, kr] = 1
log.timer("ao2mo transformation", *cput0)