def init_amps(self, eris=None):
time0 = time.clock(), time.time()
if eris is None:
eris = self.ao2mo(self.mo_coeff)
nocca, noccb = self.nocc
fova = eris.focka[:nocca,nocca:]
fovb = eris.fockb[:noccb,noccb:]
mo_ea_o = eris.mo_energy[0][:nocca]
mo_ea_v = eris.mo_energy[0][nocca:]
mo_eb_o = eris.mo_energy[1][:noccb]
mo_eb_v = eris.mo_energy[1][noccb:]
eia_a = lib.direct_sum('i-a->ia', mo_ea_o, mo_ea_v)
eia_b = lib.direct_sum('i-a->ia', mo_eb_o, mo_eb_v)
t1a = fova.conj() / eia_a
t1b = fovb.conj() / eia_b
eris_ovov = np.asarray(eris.ovov)
eris_OVOV = np.asarray(eris.OVOV)
eris_ovOV = np.asarray(eris.ovOV)
t2aa = eris_ovov.transpose(0,2,1,3) / lib.direct_sum('ia+jb->ijab', eia_a, eia_a)
t2ab = eris_ovOV.transpose(0,2,1,3) / lib.direct_sum('ia+jb->ijab', eia_a, eia_b)
t2bb = eris_OVOV.transpose(0,2,1,3) / lib.direct_sum('ia+jb->ijab', eia_b, eia_b)
t2aa = t2aa - t2aa.transpose(0,1,3,2)
t2bb = t2bb - t2bb.transpose(0,1,3,2)
e = np.einsum('iJaB,iaJB', t2ab, eris_ovOV)
e += 0.25*np.einsum('ijab,iajb', t2aa, eris_ovov)
e -= 0.25*np.einsum('ijab,ibja', t2aa, eris_ovov)
e += 0.25*np.einsum('ijab,iajb', t2bb, eris_OVOV)
e -= 0.25*np.einsum('ijab,ibja', t2bb, eris_OVOV)
self.emp2 = e.real
logger.info(self, 'Init t2, MP2 energy = %.15g', self.emp2)
logger.timer(self, 'init mp2', *time0)
return self.emp2, (t1a,t1b), (t2aa,t2ab,t2bb)
def make_intermediates(mycc, t1, t2, eris):
saved = ccsd_lambda.make_intermediates(mycc, t1, t2, eris)
nocc, nvir = t1.shape
eris_ovvv = _cp(eris.ovvv)
eris_ovvv = lib.unpack_tril(eris_ovvv.reshape(nocc*nvir,-1))
eris_ovvv = eris_ovvv.reshape(nocc,nvir,nvir,nvir)
mo_e = mycc._scf.mo_energy
eia = lib.direct_sum('i-a->ia',mo_e[:nocc], mo_e[nocc:])
d3 = lib.direct_sum('ia,jb,kc->ijkabc', eia, eia, eia)
eris_ovoo = eris.ovoo
w =(numpy.einsum('iabf,kjcf->ijkabc', eris_ovvv, t2)
- numpy.einsum('iajm,mkbc->ijkabc', eris_ovoo, t2)) / d3
v = numpy.einsum('iajb,kc->ijkabc', eris.ovov, t1) / d3 * .5
w = p6_(w)
v = p6_(v)
rwv = r6_(w*2+v)
jov = numpy.einsum('jbkc,ijkabc->ia', eris.ovov, r6_(w))
joovv = numpy.einsum('iabf,ijkabc->kjcf', eris_ovvv, rwv)
joovv-= numpy.einsum('iajm,ijkabc->mkbc', eris.ovoo, rwv)
joovv = joovv + joovv.transpose(1,0,3,2)
saved.jov = jov
saved.joovv = joovv
return saved
def solve_mo1(sscobj, mo_energy=None, mo_coeff=None, mo_occ=None,
h1=None, s1=None, with_cphf=None):
cput1 = (time.clock(), time.time())
log = logger.Logger(sscobj.stdout, sscobj.verbose)
if mo_energy is None: mo_energy = sscobj._scf.mo_energy
if mo_coeff is None: mo_coeff = sscobj._scf.mo_coeff
if mo_occ is None: mo_occ = sscobj._scf.mo_occ
if with_cphf is None: with_cphf = sscobj.cphf
mol = sscobj.mol
if h1 is None:
atmlst = sorted(set([j for i,j in sscobj.nuc_pair]))
h1a, h1b = make_h1_pso(mol, sscobj._scf.mo_coeff, mo_occ, atmlst)
else:
h1a, h1b = h1
h1a = numpy.asarray(h1a)
h1b = numpy.asarray(h1b)
if with_cphf:
if callable(with_cphf):
vind = with_cphf
else:
vind = gen_vind(sscobj._scf, mo_coeff, mo_occ)
mo1, mo_e1 = ucphf.solve(vind, mo_energy, mo_occ, (h1a,h1b), None,
sscobj.max_cycle_cphf, sscobj.conv_tol,
verbose=log)
else:
eai_aa = lib.direct_sum('i-a->ai', mo_energy[0][mo_occ[0]>0], mo_energy[0][mo_occ[0]==0])
eai_bb = lib.direct_sum('i-a->ai', mo_energy[1][mo_occ[1]>0], mo_energy[1][mo_occ[1]==0])
mo1 = (h1a * (1/eai_aa), h1b * (1/eai_bb))
mo_e1 = None
logger.timer(sscobj, 'solving mo1 eqn', *cput1)
return mo1, mo_e1
def gamma1_intermediates(mycc, t1, t2, l1, l2, eris=None):
doo, dov, dvo, dvv = ccsd_rdm.gamma1_intermediates(mycc, t1, t2, l1, l2)
if eris is None: eris = ccsd._ERIS(mycc)
nocc, nvir = t1.shape
eris_ovvv = _cp(eris.ovvv)
eris_ovvv = _ccsd.unpack_tril(eris_ovvv.reshape(nocc*nvir,-1))
eris_ovvv = eris_ovvv.reshape(nocc,nvir,nvir,nvir)
mo_e = mycc._scf.mo_energy
eia = lib.direct_sum('i-a->ia',mo_e[:nocc], mo_e[nocc:])
d3 = lib.direct_sum('ia,jb,kc->ijkabc', eia, eia, eia)
eris_ovoo = eris.ovoo
w =(numpy.einsum('iabf,kjcf->ijkabc', eris_ovvv, t2)
- numpy.einsum('iajm,mkbc->ijkabc', eris_ovoo, t2)) / d3
v = numpy.einsum('iajb,kc->ijkabc', eris.ovov, t1) / d3 * .5
w = p6_(w)
v = p6_(v)
wv = w+v
rw = r6_(w)
goo =-numpy.einsum('iklabc,jklabc->ij', wv, rw) * .5
gvv = numpy.einsum('ijkacd,ijkbcd->ab', wv, rw) * .5
doo += goo
dvv += gvv
return doo, dov, dvo, dvv
def gamma2_intermediates(mycc, t1, t2, l1, l2, eris=None):
dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov = \
ccsd_rdm.gamma2_intermediates(mycc, t1, t2, l1, l2)
if eris is None: eris = ccsd._ERIS(mycc)
nocc, nvir = t1.shape
eris_ovvv = _cp(eris.ovvv)
eris_ovvv = _ccsd.unpack_tril(eris_ovvv.reshape(nocc*nvir,-1))
eris_ovvv = eris_ovvv.reshape(nocc,nvir,nvir,nvir)
mo_e = mycc._scf.mo_energy
eia = lib.direct_sum('i-a->ia',mo_e[:nocc], mo_e[nocc:])
d3 = lib.direct_sum('ia,jb,kc->ijkabc', eia, eia, eia)
eris_ovoo = eris.ovoo
w =(numpy.einsum('iabf,kjcf->ijkabc', eris_ovvv, t2)
- numpy.einsum('iajm,mkbc->ijkabc', eris_ovoo, t2)) / d3
v = numpy.einsum('iajb,kc->ijkabc', eris.ovov, t1) / d3 * .5
w = p6_(w)
v = p6_(v)
rw = r6_(w)
rwv = r6_(w*2+v)
dovov += numpy.einsum('kc,ijkabc->iajb', t1, rw) * .5
dooov -= numpy.einsum('mkbc,ijkabc->jmia', t2, rwv)
# Note "dovvv +=" also changes the value of dvvov
dovvv += numpy.einsum('kjcf,ijkabc->iabf', t2, rwv)
dvvov = dovvv.transpose(2,3,0,1)
return dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov
def kernel(mp, mo_energy, mo_coeff, nocc, ioblk=256, verbose=None):
nmo = mo_coeff.shape[1]
nvir = nmo - nocc
auxmol = df.incore.format_aux_basis(mp.mol, mp.auxbasis)
naoaux = auxmol.nao_nr()
iolen = max(int(ioblk*1e6/8/(nvir*nocc)), 160)
eia = lib.direct_sum('i-a->ia', mo_energy[:nocc], mo_energy[nocc:])
t2 = None
emp2 = 0
with mp.ao2mo(mo_coeff, nocc) as fov:
for p0, p1 in prange(0, naoaux, iolen):
logger.debug(mp, 'Load cderi block %d:%d', p0, p1)
qov = numpy.array(fov[p0:p1], copy=False)
for i in range(nocc):
buf = numpy.dot(qov[:,i*nvir:(i+1)*nvir].T,
qov).reshape(nvir,nocc,nvir)
gi = numpy.array(buf, copy=False)
gi = gi.reshape(nvir,nocc,nvir).transpose(1,2,0)
t2i = gi/lib.direct_sum('jb+a->jba', eia, eia[i])
# 2*ijab-ijba
theta = gi*2 - gi.transpose(0,2,1)
emp2 += numpy.einsum('jab,jab', t2i, theta)
return emp2, t2
def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2,
verbose=logger.NOTE):
if mo_energy is None or mo_coeff is None:
moidx = mp.get_frozen_mask()
mo_coeff = None
mo_energy = (mp.mo_energy[0][moidx[0]], mp.mo_energy[1][moidx[1]])
else:
# For backward compatibility. In pyscf-1.4 or earlier, mp.frozen is
# not supported when mo_energy or mo_coeff is given.
assert(mp.frozen is 0 or mp.frozen is None)
if eris is None: eris = mp.ao2mo(mo_coeff)
nocca, noccb = mp.get_nocc()
nmoa, nmob = mp.get_nmo()
nvira, nvirb = nmoa-nocca, nmob-noccb
mo_ea, mo_eb = mo_energy
eia_a = mo_ea[:nocca,None] - mo_ea[None,nocca:]
eia_b = mo_eb[:noccb,None] - mo_eb[None,noccb:]
if with_t2:
dtype = eris.ovov.dtype
t2aa = numpy.empty((nocca,nocca,nvira,nvira), dtype=dtype)
t2ab = numpy.empty((nocca,noccb,nvira,nvirb), dtype=dtype)
t2bb = numpy.empty((noccb,noccb,nvirb,nvirb), dtype=dtype)
t2 = (t2aa,t2ab,t2bb)
else:
t2 = None
emp2 = 0.0
for i in range(nocca):
eris_ovov = numpy.asarray(eris.ovov[i*nvira:(i+1)*nvira])
eris_ovov = eris_ovov.reshape(nvira,nocca,nvira).transpose(1,0,2)
t2i = eris_ovov.conj()/lib.direct_sum('a+jb->jab', eia_a[i], eia_a)
emp2 += numpy.einsum('jab,jab', t2i, eris_ovov) * .5
emp2 -= numpy.einsum('jab,jba', t2i, eris_ovov) * .5
if with_t2:
t2aa[i] = t2i - t2i.transpose(0,2,1)
eris_ovov = numpy.asarray(eris.ovOV[i*nvira:(i+1)*nvira])
eris_ovov = eris_ovov.reshape(nvira,noccb,nvirb).transpose(1,0,2)
t2i = eris_ovov.conj()/lib.direct_sum('a+jb->jab', eia_a[i], eia_b)
emp2 += numpy.einsum('JaB,JaB', t2i, eris_ovov)
if with_t2:
t2ab[i] = t2i
for i in range(noccb):
eris_ovov = numpy.asarray(eris.OVOV[i*nvirb:(i+1)*nvirb])
eris_ovov = eris_ovov.reshape(nvirb,noccb,nvirb).transpose(1,0,2)
t2i = eris_ovov.conj()/lib.direct_sum('a+jb->jab', eia_b[i], eia_b)
emp2 += numpy.einsum('jab,jab', t2i, eris_ovov) * .5
emp2 -= numpy.einsum('jab,jba', t2i, eris_ovov) * .5
if with_t2:
t2bb[i] = t2i - t2i.transpose(0,2,1)
return emp2.real, t2
def get_sigma_element(gw, omega, tdm_p, tdm_q, td_e, eta=None, vir_sgn=1):
if eta is None:
eta = gw.eta
nocc = gw.nocc
evi = lib.direct_sum('v-i->vi', td_e, gw._scf.mo_energy[:nocc])
eva = lib.direct_sum('v+a->va', td_e, gw._scf.mo_energy[nocc:])
sigma = np.sum( tdm_p[:,:nocc]*tdm_q[:,:nocc]/(omega + evi - 1j*eta) )
sigma += np.sum( tdm_p[:,nocc:]*tdm_q[:,nocc:]/(omega - eva + vir_sgn*1j*eta) )
return sigma
def solve_withs1(fvind, mo_energy, mo_occ, h1, s1,
max_cycle=20, tol=1e-9, hermi=False, verbose=logger.WARN):
'''For field dependent basis. First order overlap matrix is non-zero.
The first order orbitals are set to
C^1_{ij} = -1/2 S1
e1 = h1 - s1*e0 + (e0_j-e0_i)*c1 + vhf[c1]
Kwargs:
hermi : boolean
Whether the matrix defined by fvind is Hermitian or not.
Returns:
First order orbital coefficients (in MO basis) and first order orbital
energy matrix
'''
log = logger.new_logger(verbose=verbose)
t0 = (time.clock(), time.time())
occidx = mo_occ > 0
viridx = mo_occ == 0
e_a = mo_energy[viridx]
e_i = mo_energy[occidx]
e_ai = 1 / lib.direct_sum('a-i->ai', e_a, e_i)
nvir, nocc = e_ai.shape
nmo = nocc + nvir
s1 = s1.reshape(-1,nmo,nocc)
hs = mo1base = h1.reshape(-1,nmo,nocc) - s1*e_i
mo_e1 = hs[:,occidx,:].copy()
mo1base[:,viridx] *= -e_ai
mo1base[:,occidx] = -s1[:,occidx] * .5
def vind_vo(mo1):
v = fvind(mo1.reshape(h1.shape)).reshape(-1,nmo,nocc)
v[:,viridx,:] *= e_ai
v[:,occidx,:] = 0
return v.ravel()
mo1 = lib.krylov(vind_vo, mo1base.ravel(),
tol=tol, max_cycle=max_cycle, hermi=hermi, verbose=log)
mo1 = mo1.reshape(mo1base.shape)
log.timer('krylov solver in CPHF', *t0)
v1mo = fvind(mo1.reshape(h1.shape)).reshape(-1,nmo,nocc)
mo1[:,viridx] = mo1base[:,viridx] - v1mo[:,viridx]*e_ai
# mo_e1 has the same symmetry as the first order Fock matrix (hermitian or
# anti-hermitian). mo_e1 = v1mo - s1*lib.direct_sum('i+j->ij',e_i,e_i)
mo_e1 += mo1[:,occidx] * lib.direct_sum('i-j->ij', e_i, e_i)
mo_e1 += v1mo[:,occidx,:]
if h1.ndim == 3:
return mo1, mo_e1
else:
return mo1.reshape(h1.shape), mo_e1.reshape(nocc,nocc)
def get_init_guess(self, eris=None, nroots=1, diag=None):
if eris is None: eris = self.ao2mo(self.mo_coeff)
nocca, noccb = self.nocc
mo_ea, mo_eb = eris.mo_energy
eia_a = mo_ea[:nocca,None] - mo_ea[None,nocca:]
eia_b = mo_eb[:noccb,None] - mo_eb[None,noccb:]
t1a = eris.focka[:nocca,nocca:].conj() / eia_a
t1b = eris.fockb[:noccb,noccb:].conj() / eia_b
eris_ovov = _cp(eris.ovov)
eris_ovOV = _cp(eris.ovOV)
eris_OVOV = _cp(eris.OVOV)
t2aa = eris_ovov.transpose(0,2,1,3) - eris_ovov.transpose(0,2,3,1)
t2bb = eris_OVOV.transpose(0,2,1,3) - eris_OVOV.transpose(0,2,3,1)
t2ab = eris_ovOV.transpose(0,2,1,3).copy()
t2aa = t2aa.conj()
t2ab = t2ab.conj()
t2bb = t2bb.conj()
t2aa /= lib.direct_sum('ia+jb->ijab', eia_a, eia_a)
t2ab /= lib.direct_sum('ia+jb->ijab', eia_a, eia_b)
t2bb /= lib.direct_sum('ia+jb->ijab', eia_b, eia_b)
emp2 = numpy.einsum('iajb,ijab', eris_ovov, t2aa) * .25
emp2 -= numpy.einsum('jaib,ijab', eris_ovov, t2aa) * .25
emp2 += numpy.einsum('iajb,ijab', eris_OVOV, t2bb) * .25
emp2 -= numpy.einsum('jaib,ijab', eris_OVOV, t2bb) * .25
emp2 += numpy.einsum('iajb,ijab', eris_ovOV, t2ab)
self.emp2 = emp2.real
logger.info(self, 'Init t2, MP2 energy = %.15g', self.emp2)
if abs(emp2) < 1e-3 and (abs(t1a).sum()+abs(t1b).sum()) < 1e-3:
t1a = 1e-1 / eia_a
t1b = 1e-1 / eia_b
ci_guess = amplitudes_to_cisdvec(1, (t1a,t1b), (t2aa,t2ab,t2bb))
if nroots > 1:
civec_size = ci_guess.size
ci1_size = t1a.size + t1b.size
dtype = ci_guess.dtype
nroots = min(ci1_size+1, nroots)
if diag is None:
idx = range(1, nroots)
else:
idx = diag[:ci1_size+1].argsort()[1:nroots] # exclude HF determinant
ci_guess = [ci_guess]
for i in idx:
g = numpy.zeros(civec_size, dtype)
g[i] = 1.0
ci_guess.append(g)
return self.emp2, ci_guess
def update_amps(mycc, t1, t2, l1, l2, eris=None, saved=None):
if eris is None: eris = ccsd._ERIS(mycc)
if saved is None: saved = make_intermediates(mycc, t1, t2, eris)
nocc, nvir = t1.shape
l1, l2 = ccsd_lambda.update_amps(mycc, t1, t2, l1, l2, eris, saved)
mo_e = eris.fock.diagonal()
eia = lib.direct_sum('i-a->ia', mo_e[:nocc], mo_e[nocc:])
l1 += saved.jov/eia * .5
eijab = lib.direct_sum('ia+jb->ijab', eia, eia)
l2 += (saved.joovv*(2./3)+saved.joovv.transpose(1,0,2,3)*(1./3)) / eijab
return l1, l2
def make_intermediates(mycc, t1, t2, eris):
imds = ccsd_lambda.make_intermediates(mycc, t1, t2, eris)
nocc, nvir = t1.shape
eris_ovvv = numpy.asarray(eris.get_ovvv())
eris_ovoo = numpy.asarray(eris.ovoo)
eris_ovov = numpy.asarray(eris.ovov)
mo_e = eris.mo_energy
eia = lib.direct_sum('i-a->ia', mo_e[:nocc], mo_e[nocc:])
d3 = lib.direct_sum('ia,jb,kc->ijkabc', eia, eia, eia)
def p6(t):
t1 = t + t.transpose(0,2,1,3,5,4)
return t1 + t1.transpose(1,0,2,4,3,5) + t1.transpose(1,2,0,4,5,3)
def r6(w):
return (4 * w + w.transpose(0,1,2,4,5,3) + w.transpose(0,1,2,5,3,4)
- 2 * w.transpose(0,1,2,5,4,3) - 2 * w.transpose(0,1,2,3,5,4)
- 2 * w.transpose(0,1,2,4,3,5))
w =(numpy.einsum('iafb,kjcf->ijkabc', eris_ovvv.conj(), t2)
- numpy.einsum('iajm,mkbc->ijkabc', eris_ovoo.conj(), t2)) / d3
v =(numpy.einsum('iajb,kc->ijkabc', eris_ovov.conj(), t1)
+ numpy.einsum('ck,ijab->ijkabc', eris.fock[nocc:,:nocc], t2)) / d3
w = p6(w)
v = p6(v)
imds.l1_t = numpy.einsum('jbkc,ijkabc->ia', eris_ovov, r6(w)).conj() / eia * .5
def as_r6(m):
# When making derivative over t2, r6 should be called on the 6-index
# tensor. It gives the equation for lambda2, but not corresponding to
# the lambda equation used by RCCSD-lambda code. A transformation was
# applied in RCCSD-lambda equation F(lambda)_{ijab} = 0:
# 2/3 * # F(lambda)_{ijab} + 1/3 * F(lambda)_{jiab} = 0
# Combining this transformation with r6 operation, leads to the
# transformation code below
return m * 2 - m.transpose(0,1,2,5,4,3) - m.transpose(0,1,2,3,5,4)
m = as_r6(w * 2 + v * .5)
joovv = numpy.einsum('kfbe,ijkaef->ijab', eris_ovvv, m.conj())
joovv-= numpy.einsum('ncmj,imnabc->ijab', eris_ovoo, m.conj())
joovv = joovv + joovv.transpose(1,0,3,2)
rw = as_r6(w)
joovv+= numpy.einsum('kc,ijkabc->ijab', eris.fock[:nocc,nocc:], rw.conj())
imds.l2_t = joovv / lib.direct_sum('ia+jb->ijab', eia, eia)
return imds
def solve_withs1(fvind, mo_energy, mo_occ, h1, s1,
max_cycle=20, tol=1e-9, hermi=False, verbose=logger.WARN):
''' C^1_{ij} = -1/2 S1
e1 = h1 - s1*e0 + (e0_j-e0_i)*c1 + vhf[c1]
'''
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(sys.stdout, verbose)
t0 = (time.clock(), time.time())
occidx = mo_occ > 0
viridx = mo_occ == 0
e_a = mo_energy[viridx]
e_i = mo_energy[occidx]
e_ai = 1 / lib.direct_sum('a-i->ai', e_a, e_i)
nvir, nocc = e_ai.shape
nmo = nocc + nvir
# Do not reshape h1 because h1 may be a 2D array (nvir,nocc)
s1 = s1.reshape(-1,nmo,nocc)
hs = mo1base = h1.reshape(-1,nmo,nocc) - s1*e_i
mo_e1 = hs[:,occidx,:].copy()
mo1base[:,viridx] *= -e_ai
mo1base[:,occidx] = -s1[:,occidx] * .5
def vind_vo(mo1):
v = fvind(mo1.reshape(h1.shape)).reshape(-1,nmo,nocc)
v[:,viridx,:] *= e_ai
v[:,occidx,:] = 0
return v.ravel()
mo1 = lib.krylov(vind_vo, mo1base.ravel(),
tol=tol, max_cycle=max_cycle, hermi=hermi, verbose=log)
mo1 = mo1.reshape(mo1base.shape)
log.timer('krylov solver in CPHF', *t0)
v_mo = fvind(mo1.reshape(h1.shape)).reshape(-1,nmo,nocc)
mo1[:,viridx] = mo1base[:,viridx] - v_mo[:,viridx]*e_ai
mo_e1 += mo1[:,occidx] * lib.direct_sum('i-j->ij', e_i, e_i)
mo_e1 += v_mo[:,occidx,:]
if h1.ndim == 3:
return mo1, mo_e1
else:
return mo1.reshape(h1.shape), mo_e1.reshape(nocc,nocc)
def kernel(myci, eris, ci0=None, max_cycle=50, tol=1e-8,
verbose=logger.INFO):
mol = myci.mol
nmo = myci.nmo
nocc = myci.nocc
mo_energy = eris.fock.diagonal()
diag = make_diagonal(mol, mo_energy, eris, nocc)
ehf = diag[0]
diag -= ehf
if ci0 is None:
# MP2 initial guess
nvir = nmo - nocc
e_i = mo_energy[:nocc]
e_a = mo_energy[nocc:]
ci0 = numpy.zeros(1+nocc*nvir+(nocc*nvir)**2)
ci0[0] = 1
t2 = 2*eris.voov.transpose(1,2,0,3) - eris.voov.transpose(1,2,3,0)
t2 /= lib.direct_sum('i+j-a-b', e_i, e_i, e_a, e_a)
ci0[1+nocc*nvir:] = t2.ravel()
def op(x):
return contract(myci, x, eris)
def precond(x, e, *args):
return x / (diag - e)
def cisd_dot(x1, x2):
return dot(x1, x2, nocc, nvir)
ecisd, ci = lib.davidson(op, ci0, precond, max_cycle=max_cycle, tol=tol,
dot=cisd_dot, verbose=verbose)
conv = True # It should be checked in lib.davidson function
return conv, ecisd, ci
def _gamma1_intermediates(mp, t2=None, eris=None):
if t2 is None: t2 = mp.t2
nmo = mp.nmo
nocc = mp.nocc
nvir = nmo - nocc
if t2 is None:
if eris is None: eris = mp.ao2mo()
mo_energy = _mo_energy_without_core(mp, mp.mo_energy)
eia = mo_energy[:nocc,None] - mo_energy[None,nocc:]
dtype = eris.ovov.dtype
else:
dtype = t2.dtype
dm1occ = numpy.zeros((nocc,nocc), dtype=dtype)
dm1vir = numpy.zeros((nvir,nvir), dtype=dtype)
for i in range(nocc):
if t2 is None:
gi = numpy.asarray(eris.ovov[i*nvir:(i+1)*nvir])
gi = gi.reshape(nvir,nocc,nvir).transpose(1,0,2)
t2i = gi.conj()/lib.direct_sum('jb+a->jba', eia, eia[i])
else:
t2i = t2[i]
l2i = t2i.conj()
dm1vir += numpy.einsum('jca,jcb->ba', l2i, t2i) * 2 \
- numpy.einsum('jca,jbc->ba', l2i, t2i)
dm1occ += numpy.einsum('iab,jab->ij', l2i, t2i) * 2 \
- numpy.einsum('iab,jba->ij', l2i, t2i)
return -dm1occ, dm1vir
def get_vind(self, zs):
mol = self.mol
mo_coeff = self._scf.mo_coeff
mo_energy = self._scf.mo_energy
nao, nmo = mo_coeff.shape
nocc = (self._scf.mo_occ>0).sum()
nvir = nmo - nocc
orbv = mo_coeff[:,nocc:]
orbo = mo_coeff[:,:nocc]
eai = lib.direct_sum('a-i->ai', mo_energy[nocc:], mo_energy[:nocc])
dai = numpy.sqrt(eai).ravel()
nz = len(zs)
dmvo = numpy.empty((nz,nao,nao))
for i, z in enumerate(zs):
dm = reduce(numpy.dot, (orbv, (dai*z).reshape(nvir,nocc), orbo.T))
dmvo[i] = dm + dm.T # +cc for A+B and K_{ai,jb} in A == K_{ai,bj} in B
mem_now = lib.current_memory()[0]
max_memory = max(2000, self.max_memory*.9-mem_now)
v1ao = _contract_xc_kernel(self, self._scf.xc, dmvo,
singlet=self.singlet, max_memory=max_memory)
if self.singlet:
vj = self._scf.get_j(mol, dmvo, hermi=1)
v1ao += vj * 2
v1vo = _ao2mo.nr_e2(v1ao, mo_coeff, (nocc,nmo,0,nocc)).reshape(-1,nvir*nocc)
edai = eai.ravel() * dai
for i, z in enumerate(zs):
# numpy.sqrt(eai) * (eai*dai*z + v1vo)
v1vo[i] += edai*z
v1vo[i] *= dai
return v1vo.reshape(nz,-1)
def gen_hop_rhf_external(mf):
mol = mf.mol
mo_coeff = mf.mo_coeff
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
nmo = mo_coeff.shape[1]
nocc = numpy.count_nonzero(mo_occ)
nvir = nmo - nocc
nov = nocc * nvir
eri_mo = ao2mo.full(mol, mo_coeff)
eri_mo = ao2mo.restore(1, eri_mo, nmo)
eai = lib.direct_sum('a-i->ai', mo_energy[nocc:], mo_energy[:nocc])
# A
h = numpy.einsum('ckld->kcld', eri_mo[nocc:,:nocc,:nocc,nocc:]) * 2
h-= numpy.einsum('cdlk->kcld', eri_mo[nocc:,nocc:,:nocc,:nocc])
for a in range(nvir):
for i in range(nocc):
h[i,a,i,a] += eai[a,i]
# B
h-= numpy.einsum('ckdl->kcld', eri_mo[nocc:,:nocc,nocc:,:nocc]) * 2
h+= numpy.einsum('cldk->kcld', eri_mo[nocc:,:nocc,nocc:,:nocc])
h1 = h.transpose(1,0,3,2).reshape(nov,nov)
def hop1(x):
return h1.dot(x)
h =-numpy.einsum('cdlk->kcld', eri_mo[nocc:,nocc:,:nocc,:nocc])
for a in range(nvir):
for i in range(nocc):
h[i,a,i,a] += eai[a,i]
h-= numpy.einsum('cldk->kcld', eri_mo[nocc:,:nocc,nocc:,:nocc])
h2 = h.transpose(1,0,3,2).reshape(nov,nov)
def hop2(x):
return h2.dot(x)
return hop1, hop2
def rhf_internal(mf, verbose=None):
log = logger.new_logger(mf, verbose)
mol = mf.mol
mo_coeff = mf.mo_coeff
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
nmo = mo_coeff.shape[1]
nocc = numpy.count_nonzero(mo_occ)
nvir = nmo - nocc
eri_mo = ao2mo.full(mol, mo_coeff)
eri_mo = ao2mo.restore(1, eri_mo, nmo)
eai = lib.direct_sum('a-i->ai', mo_energy[nocc:], mo_energy[:nocc])
# A
h = numpy.einsum('ckld->kcld', eri_mo[nocc:,:nocc,:nocc,nocc:]) * 2
h-= numpy.einsum('cdlk->kcld', eri_mo[nocc:,nocc:,:nocc,:nocc])
for a in range(nvir):
for i in range(nocc):
h[i,a,i,a] += eai[a,i]
# B
h+= numpy.einsum('ckdl->kcld', eri_mo[nocc:,:nocc,nocc:,:nocc]) * 2
h-= numpy.einsum('cldk->kcld', eri_mo[nocc:,:nocc,nocc:,:nocc])
nov = nocc * nvir
e = scipy.linalg.eigh(h.reshape(nov,nov))[0]
log.debug('rhf_internal: lowest eigs = %s', e[e<=max(e[0],1e-5)])
if e[0] < -1e-5:
log.log('RHF wavefunction has an internal instablity')
else:
log.log('RHF wavefunction is stable in the intenral stablity analysis')
def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2,
verbose=logger.NOTE):
if mo_energy is None or mo_coeff is None:
mo_coeff = None
mo_energy = mp.mo_energy[mp.get_frozen_mask()]
else:
# For backward compatibility. In pyscf-1.4 or earlier, mp.frozen is
# not supported when mo_energy or mo_coeff is given.
assert(mp.frozen is 0 or mp.frozen is None)
if eris is None: eris = mp.ao2mo(mo_coeff)
nocc = mp.nocc
nvir = mp.nmo - nocc
moidx = mp.get_frozen_mask()
eia = mo_energy[:nocc,None] - mo_energy[None,nocc:]
if with_t2:
t2 = numpy.empty((nocc,nocc,nvir,nvir), dtype=eris.oovv.dtype)
else:
t2 = None
emp2 = 0
for i in range(nocc):
gi = numpy.asarray(eris.oovv[i]).reshape(nocc,nvir,nvir)
t2i = gi.conj()/lib.direct_sum('jb+a->jba', eia, eia[i])
emp2 += numpy.einsum('jab,jab', t2i, gi) * .25
if with_t2:
t2[i] = t2i
return emp2.real, t2
def init_amps(self, eris):
time0 = time.clock(), time.time()
nocc = self.nocc()
nvir = self.nmo() - nocc
nkpts = self.nkpts
t1 = numpy.zeros((nkpts, nocc, nvir), dtype=numpy.complex128)
t2 = numpy.zeros((nkpts, nkpts, nkpts, nocc, nocc, nvir, nvir), dtype=numpy.complex128)
woovv = numpy.empty((nkpts, nkpts, nkpts, nocc, nocc, nvir, nvir), dtype=numpy.complex128)
self.emp2 = 0
foo = eris.fock[:, :nocc, :nocc].copy()
fvv = eris.fock[:, nocc:, nocc:].copy()
eris_oovv = eris.oovv.copy()
eia = numpy.zeros((nocc, nvir))
eijab = numpy.zeros((nocc, nocc, nvir, nvir))
kconserv = self.kconserv
for ki in range(nkpts):
for kj in range(nkpts):
for ka in range(nkpts):
kb = kconserv[ki, ka, kj]
eia = np.diagonal(foo[ki]).reshape(-1, 1) - np.diagonal(fvv[ka])
ejb = np.diagonal(foo[kj]).reshape(-1, 1) - np.diagonal(fvv[kb])
eijab = lib.direct_sum("ia,jb->ijab", eia, ejb)
woovv[ki, kj, ka] = 2 * eris_oovv[ki, kj, ka] - eris_oovv[ki, kj, kb].transpose(0, 1, 3, 2)
t2[ki, kj, ka] = eris_oovv[ki, kj, ka] / eijab
t2 = numpy.conj(t2)
self.emp2 = numpy.einsum("pqrijab,pqrijab", t2, woovv).real
self.emp2 /= nkpts
logger.info(self, "Init t2, MP2 energy = %.15g", self.emp2)
logger.timer(self, "init mp2", *time0)
return self.emp2, t1, t2
def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2,
verbose=logger.NOTE):
if mo_energy is None or mo_coeff is None:
if mp.mo_energy is None or mp.mo_coeff is None:
raise RuntimeError('mo_coeff, mo_energy are not initialized.\n'
'You may need to call mf.kernel() to generate them.')
mo_coeff = None
mo_energy = _mo_energy_without_core(mp, mp.mo_energy)
else:
# For backward compatibility. In pyscf-1.4 or earlier, mp.frozen is
# not supported when mo_energy or mo_coeff is given.
assert(mp.frozen is 0 or mp.frozen is None)
if eris is None: eris = mp.ao2mo(mo_coeff)
nocc = mp.nocc
nvir = mp.nmo - nocc
eia = mo_energy[:nocc,None] - mo_energy[None,nocc:]
if with_t2:
t2 = numpy.empty((nocc,nocc,nvir,nvir), dtype=eris.ovov.dtype)
else:
t2 = None
emp2 = 0
for i in range(nocc):
gi = numpy.asarray(eris.ovov[i*nvir:(i+1)*nvir])
gi = gi.reshape(nvir,nocc,nvir).transpose(1,0,2)
t2i = gi.conj()/lib.direct_sum('jb+a->jba', eia, eia[i])
emp2 += numpy.einsum('jab,jab', t2i, gi) * 2
emp2 -= numpy.einsum('jab,jba', t2i, gi)
if with_t2:
t2[i] = t2i
return emp2.real, t2
def solve_nos1(fvind, mo_energy, mo_occ, h1,
max_cycle=20, tol=1e-9, hermi=False, verbose=logger.WARN):
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(sys.stdout, verbose)
t0 = (time.clock(), time.time())
e_a = mo_energy[mo_occ==0]
e_i = mo_energy[mo_occ>0]
e_ai = 1 / lib.direct_sum('a-i->ai', e_a, e_i)
nocc = e_i.size
nvir = e_a.size
nmo = nocc + nvir
mo1base = h1 * -e_ai
def vind_vo(mo1):
v = fvind(mo1.reshape(h1.shape)).reshape(h1.shape)
v *= e_ai
return v.ravel()
mo1 = lib.krylov(vind_vo, mo1base.ravel(),
tol=tol, max_cycle=max_cycle, hermi=hermi, verbose=log)
log.timer('krylov solver in CPHF', *t0)
return mo1.reshape(h1.shape), None
def kernel(cc, eris, t1=None, t2=None, max_memory=2000, verbose=logger.INFO):
assert(isinstance(eris, gccsd._PhysicistsERIs))
if t1 is None or t2 is None:
t1, t2 = cc.t1, cc.t2
nocc, nvir = t1.shape
bcei = numpy.asarray(eris.ovvv).conj().transpose(3,2,1,0)
majk = numpy.asarray(eris.ooov).conj().transpose(2,3,0,1)
bcjk = numpy.asarray(eris.oovv).conj().transpose(2,3,0,1)
mo_e = eris.fock.diagonal().real
eia = mo_e[:nocc,None] - mo_e[nocc:]
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eia, eia, eia)
t3c =(numpy.einsum('jkae,bcei->ijkabc', t2, bcei)
- numpy.einsum('imbc,majk->ijkabc', t2, majk))
t3c = t3c - t3c.transpose(0,1,2,4,3,5) - t3c.transpose(0,1,2,5,4,3)
t3c = t3c - t3c.transpose(1,0,2,3,4,5) - t3c.transpose(2,1,0,3,4,5)
t3c /= d3
# e4 = numpy.einsum('ijkabc,ijkabc,ijkabc', t3c.conj(), d3, t3c) / 36
# sia = numpy.einsum('jkbc,ijkabc->ia', eris.oovv, t3c) * .25
# e5 = numpy.einsum('ia,ia', sia, t1.conj())
# et = e4 + e5
# return et
t3d = numpy.einsum('ia,bcjk->ijkabc', t1, bcjk)
t3d += numpy.einsum('ai,jkbc->ijkabc', eris.fock[nocc:,:nocc], t2)
t3d = t3d - t3d.transpose(0,1,2,4,3,5) - t3d.transpose(0,1,2,5,4,3)
t3d = t3d - t3d.transpose(1,0,2,3,4,5) - t3d.transpose(2,1,0,3,4,5)
t3d /= d3
et = numpy.einsum('ijkabc,ijkabc,ijkabc', (t3c+t3d).conj(), d3, t3c) / 36
return et
def fupdate(t1, t2, istep, normt, de, adiis):
nocc, nvir = t1.shape
nov = nocc*nvir
moidx = numpy.ones(mycc.mo_energy.size, dtype=numpy.bool)
if isinstance(mycc.frozen, (int, numpy.integer)):
moidx[:mycc.frozen] = False
else:
moidx[mycc.frozen] = False
mo_e = mycc.mo_energy[moidx]
eia = mo_e[:nocc,None] - mo_e[None,nocc:]
if (istep > mycc.diis_start_cycle and
abs(de) < mycc.diis_start_energy_diff):
if mycc.t1 is None:
mycc.t1 = t1
mycc.t2 = t2
else:
tbuf = numpy.empty(nov*(nov+1))
tbuf[:nov] = ((t1-mycc.t1)*eia).ravel()
pbuf = tbuf[nov:].reshape(nocc,nocc,nvir,nvir)
for i in range(nocc):
pbuf[i] = (t2[i]-mycc.t2[i]) * lib.direct_sum('jb,a->jba', eia, eia[i])
adiis.push_err_vec(tbuf)
tbuf = numpy.empty(nov*(nov+1))
tbuf[:nov] = t1.ravel()
tbuf[nov:] = t2.ravel()
t1.data = tbuf.data # release memory
t2.data = tbuf.data
tbuf = adiis.update(tbuf)
mycc.t1 = t1 = tbuf[:nov].reshape(nocc,nvir)
mycc.t2 = t2 = tbuf[nov:].reshape(nocc,nocc,nvir,nvir)
logger.debug(mycc, 'DIIS for step %d', istep)
return t1, t2
def get_vind(self, zs):
'''Compute Ax'''
mo_coeff = self._scf.mo_coeff
mo_energy = self._scf.mo_energy
nao, nmo = mo_coeff.shape
nocc = (self._scf.mo_occ>0).sum()
nvir = nmo - nocc
orbv = mo_coeff[:,nocc:]
orbo = mo_coeff[:,:nocc]
nz = len(zs)
dmvo = numpy.empty((nz,nao,nao))
for i, z in enumerate(zs):
dmvo[i] = reduce(numpy.dot, (orbv, z.reshape(nvir,nocc), orbo.T))
vj, vk = self._scf.get_jk(self.mol, dmvo, hermi=0)
if self.singlet:
vhf = vj*2 - vk
else:
vhf = -vk
#v1vo = numpy.asarray([reduce(numpy.dot, (orbv.T, v, orbo)) for v in vhf])
v1vo = _ao2mo.nr_e2(vhf, mo_coeff, (nocc,nmo,0,nocc)).reshape(-1,nvir*nocc)
eai = lib.direct_sum('a-i->ai', mo_energy[nocc:], mo_energy[:nocc])
eai = eai.ravel()
for i, z in enumerate(zs):
v1vo[i] += eai * z
return v1vo.reshape(nz,-1)
def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2,
verbose=logger.NOTE):
if mo_energy is None or mo_coeff is None:
mo_coeff = mp2._mo_without_core(mp, mp.mo_coeff)
mo_energy = mp2._mo_energy_without_core(mp, mp.mo_energy)
else:
# For backward compatibility. In pyscf-1.4 or earlier, mp.frozen is
# not supported when mo_energy or mo_coeff is given.
assert(mp.frozen is 0 or mp.frozen is None)
nocc = mp.nocc
nvir = mp.nmo - nocc
eia = mo_energy[:nocc,None] - mo_energy[None,nocc:]
t2 = None
emp2 = 0
for istep, qov in enumerate(mp.loop_ao2mo(mo_coeff, nocc)):
logger.debug(mp, 'Load cderi step %d', istep)
for i in range(nocc):
buf = numpy.dot(qov[:,i*nvir:(i+1)*nvir].T,
qov).reshape(nvir,nocc,nvir)
gi = numpy.array(buf, copy=False)
gi = gi.reshape(nvir,nocc,nvir).transpose(1,0,2)
t2i = gi/lib.direct_sum('jb+a->jba', eia, eia[i])
emp2 += numpy.einsum('jab,jab', t2i, gi) * 2
emp2 -= numpy.einsum('jab,jba', t2i, gi)
return emp2, t2
def solve_mo1_fc(sscobj, h1):
cput1 = (time.clock(), time.time())
log = logger.Logger(sscobj.stdout, sscobj.verbose)
mol = sscobj.mol
mo_energy = sscobj._scf.mo_energy
mo_coeff = sscobj._scf.mo_coeff
mo_occ = sscobj._scf.mo_occ
nset = len(h1)
eai = 1. / lib.direct_sum('a-i->ai', mo_energy[mo_occ==0], mo_energy[mo_occ>0])
mo1 = numpy.asarray(h1) * -eai
if not sscobj.cphf:
return mo1
orbo = mo_coeff[:,mo_occ> 0]
orbv = mo_coeff[:,mo_occ==0]
nocc = orbo.shape[1]
nvir = orbv.shape[1]
nmo = nocc + nvir
vresp = _gen_rhf_response(sscobj._scf, singlet=False, hermi=1)
mo_v_o = numpy.asarray(numpy.hstack((orbv,orbo)), order='F')
def vind(mo1):
dm1 = _dm1_mo2ao(mo1.reshape(nset,nvir,nocc), orbv, orbo*2) # *2 for double occupancy
dm1 = dm1 + dm1.transpose(0,2,1)
v1 = vresp(dm1)
v1 = _ao2mo.nr_e2(v1, mo_v_o, (0,nvir,nvir,nmo)).reshape(nset,nvir,nocc)
v1 *= eai
return v1.ravel()
mo1 = lib.krylov(vind, mo1.ravel(), tol=sscobj.conv_tol,
max_cycle=sscobj.max_cycle_cphf, verbose=log)
log.timer('solving FC CPHF eqn', *cput1)
return mo1.reshape(nset,nvir,nocc)
def _gamma1_intermediates(mycc, t1, t2, l1, l2, eris=None):
doo, dov, dvo, dvv = gccsd_rdm._gamma1_intermediates(mycc, t1, t2, l1, l2)
if eris is None: eris = mycc.ao2mo()
nocc, nvir = t1.shape
bcei = numpy.asarray(eris.ovvv).conj().transpose(3,2,1,0)
majk = numpy.asarray(eris.ooov).conj().transpose(2,3,0,1)
bcjk = numpy.asarray(eris.oovv).conj().transpose(2,3,0,1)
mo_e = eris.mo_energy
eia = mo_e[:nocc,None] - mo_e[nocc:]
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eia, eia, eia)
t3c =(numpy.einsum('jkae,bcei->ijkabc', t2, bcei)
- numpy.einsum('imbc,majk->ijkabc', t2, majk))
t3c = t3c - t3c.transpose(0,1,2,4,3,5) - t3c.transpose(0,1,2,5,4,3)
t3c = t3c - t3c.transpose(1,0,2,3,4,5) - t3c.transpose(2,1,0,3,4,5)
t3c /= d3
t3d = numpy.einsum('ia,bcjk->ijkabc', t1, bcjk)
t3d += numpy.einsum('ai,jkbc->ijkabc', eris.fock[nocc:,:nocc], t2)
t3d = t3d - t3d.transpose(0,1,2,4,3,5) - t3d.transpose(0,1,2,5,4,3)
t3d = t3d - t3d.transpose(1,0,2,3,4,5) - t3d.transpose(2,1,0,3,4,5)
t3d /= d3
goo = numpy.einsum('iklabc,jklabc->ij', (t3c+t3d).conj(), t3c) * (1./12)
gvv = numpy.einsum('ijkacd,ijkbcd->ab', t3c+t3d, t3c.conj()) * (1./12)
doo[numpy.diag_indices(nocc)] -= goo.diagonal()
dvv[numpy.diag_indices(nvir)] += gvv.diagonal()
dvo += numpy.einsum('ijab,ijkabc->ck', t2.conj(), t3c) * (1./4)
return doo, dov, dvo, dvv
def kernel(self, x0=None):
'''TDHF diagonalization with non-Hermitian eigenvalue solver
'''
self.check_sanity()
mo_energy = self._scf.mo_energy
nocc = (self._scf.mo_occ>0).sum()
eai = lib.direct_sum('a-i->ai', mo_energy[nocc:], mo_energy[:nocc])
nvir = eai.shape[0]
if x0 is None:
x0 = self.init_guess(eai, self.nstates)
precond = self.get_precond(eai.ravel())
# We only need positive eigenvalues
def pickeig(w, v, nroots, x0):
realidx = numpy.where((abs(w.imag) < 1e-6) & (w.real > 0))[0]
idx = realidx[w[realidx].real.argsort()]
return w[idx].real, v[:,idx].real, idx
w, x1 = lib.davidson_nosym1(self.get_vind, x0, precond,
tol=self.conv_tol,
nroots=self.nstates, lindep=self.lindep,
max_space=self.max_space, pick=pickeig,
verbose=self.verbose)[1:]
self.e = w
def norm_xy(z):
x, y = z.reshape(2,nvir,nocc)
norm = 2*(lib.norm(x)**2 - lib.norm(y)**2)
norm = 1/numpy.sqrt(norm)
return x*norm, y*norm
self.xy = [norm_xy(z) for z in x1]
return self.e, self.xy
def init_amps(mycc, eris=None):
eris = getattr(mycc, '_eris', None)
if eris is None:
mycc.ao2mo()
eris = mycc._eris
time0 = time.clock(), time.time()
mo_e = eris.mo_energy
nocc = mycc.nocc
nvir = mo_e.size - nocc
eia = mo_e[:nocc,None] - mo_e[None,nocc:]
t1T = eris.fock[nocc:,:nocc] / eia.T
loc0, loc1 = _task_location(nvir)
t2T = numpy.empty((loc1-loc0,nvir,nocc,nocc))
max_memory = mycc.max_memory - lib.current_memory()[0]
blksize = int(min(nvir, max(BLKMIN, max_memory*.3e6/8/(nocc**2*nvir+1))))
emp2 = 0
for p0, p1 in lib.prange(0, loc1-loc0, blksize):
eris_ovov = eris.ovov[:,p0:p1]
t2T[p0:p1] = (eris_ovov.transpose(1,3,0,2) /
lib.direct_sum('ia,jb->abij', eia[:,p0+loc0:p1+loc0], eia))
emp2 += 2 * numpy.einsum('abij,iajb', t2T[p0:p1], eris_ovov)
emp2 -= numpy.einsum('abji,iajb', t2T[p0:p1], eris_ovov)
mycc.emp2 = comm.allreduce(emp2)
logger.info(mycc, 'Init t2, MP2 energy = %.15g', mycc.emp2)
logger.timer(mycc, 'init mp2', *time0)
return mycc.emp2, t1T.T, t2T.transpose(2,3,0,1)
def solve_nos1(fvind,
mo_energy,
mo_occ,
h1,
max_cycle=20,
tol=1e-9,
hermi=False,
verbose=logger.WARN):
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(sys.stdout, verbose)
t0 = (time.clock(), time.time())
e_a = mo_energy[mo_occ == 0]
e_i = mo_energy[mo_occ > 0]
e_ai = 1 / lib.direct_sum('a-i->ai', e_a, e_i)
nocc = e_i.size
nvir = e_a.size
nmo = nocc + nvir
mo1base = h1 * -e_ai
def vind_vo(mo1):
v = fvind(mo1.reshape(h1.shape)).reshape(h1.shape)
v *= e_ai
return v.ravel()
mo1 = lib.krylov(vind_vo,
mo1base.ravel(),
tol=tol,
max_cycle=max_cycle,
hermi=hermi,
verbose=log)
log.timer('krylov solver in CPHF', *t0)
return mo1.reshape(h1.shape), None
def my_kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_eij=True):
if mo_energy is None or mo_coeff is None:
if mp.mo_energy is None or mp.mo_coeff is None:
raise RuntimeError(
'mo_coeff, mo_energy are not initialized.\n'
'You may need to call mf.kernel() to generate them.')
mo_coeff = None
mo_energy = _mo_energy_without_core(mp, mp.mo_energy)
else:
# For backward compatibility. In pyscf-1.4 or earlier, mp.frozen is
# not supported when mo_energy or mo_coeff is given.
assert (mp.frozen is 0 or mp.frozen is None)
if eris is None: eris = mp.ao2mo(mo_coeff)
nocc = mp.nocc
nvir = mp.nmo - nocc
eia = mo_energy[:nocc, None] - mo_energy[None, nocc:]
if with_eij:
eij = np.empty((nocc, nocc), dtype=eia.dtype)
else:
eij = None
emp2 = 0
for i in range(nocc):
gi = np.asarray(eris.ovov[i * nvir:(i + 1) * nvir])
gi = gi.reshape(nvir, nocc, nvir).transpose(1, 0, 2)
t2i = gi.conj() / lib.direct_sum('jb+a->jba', eia, eia[i])
tmp_eij = 2 * np.einsum('jab,jab->j', t2i, gi) - np.einsum(
'jab,jba->j', t2i, gi)
emp2 += tmp_eij.sum()
if with_eij:
eij[i] = tmp_eij
return emp2.real, eij.real
def _gamma1_intermediates(mp, mo_coeff, mo_energy, nocc, t2=None):
nmo = mo_coeff.shape[1]
nvir = nmo - nocc
eia = mo_energy[:nocc, None] - mo_energy[None, nocc:]
if (t2 is None):
t2 = []
for istep, qov in enumerate(mp.loop_ao2mo(mo_coeff, nocc)):
if (istep == 0):
dtype = qov.dtype
dm1occ = np.zeros((nocc, nocc), dtype=dtype)
dm1vir = np.zeros((nvir, nvir), dtype=dtype)
for i in range(nocc):
buf = np.dot(qov[:, i * nvir:(i + 1) * nvir].T,
qov).reshape(nvir, nocc, nvir)
gi = np.array(buf, copy=False)
gi = gi.reshape(nvir, nocc, nvir).transpose(1, 0, 2)
t2i = gi.conj() / lib.direct_sum('jb+a->jba', eia, eia[i])
t2.append(t2i)
l2i = t2i.conj()
dm1vir += np.einsum('jca,jcb->ba', l2i, t2i) * 2 \
- np.einsum('jca,jbc->ba', l2i, t2i)
dm1occ += np.einsum('iab,jab->ij', l2i, t2i) * 2 \
- np.einsum('iab,jba->ij', l2i, t2i)
else:
dtype = t2[0].dtype
dm1occ = np.zeros((nocc, nocc), dtype=dtype)
dm1vir = np.zeros((nvir, nvir), dtype=dtype)
for i in range(nocc):
t2i = t2[i]
l2i = t2i.conj()
dm1vir += np.einsum('jca,jcb->ba', l2i, t2i) * 2 \
- np.einsum('jca,jbc->ba', l2i, t2i)
dm1occ += np.einsum('iab,jab->ij', l2i, t2i) * 2 \
- np.einsum('iab,jba->ij', l2i, t2i)
return -dm1occ, dm1vir
def kernel(mp,
mo_energy=None,
mo_coeff=None,
eris=None,
with_t2=WITH_T2,
verbose=None):
if mo_energy is not None or mo_coeff is not None:
# For backward compatibility. In pyscf-1.4 or earlier, mp.frozen is
# not supported when mo_energy or mo_coeff is given.
assert (mp.frozen == 0 or mp.frozen is None)
if eris is None:
eris = mp.ao2mo(mo_coeff)
if mo_energy is None:
mo_energy = eris.mo_energy
nocc = mp.nocc
nvir = mp.nmo - nocc
#moidx = mp.get_frozen_mask()
eia = mo_energy[:nocc, None] - mo_energy[None, nocc:]
if with_t2:
t2 = numpy.empty((nocc, nocc, nvir, nvir), dtype=eris.oovv.dtype)
else:
t2 = None
emp2 = 0
for i in range(nocc):
gi = numpy.asarray(eris.oovv[i]).reshape(nocc, nvir, nvir)
t2i = gi.conj() / lib.direct_sum('jb+a->jba', eia, eia[i])
emp2 += numpy.einsum('jab,jab', t2i, gi) * .25
if with_t2:
t2[i] = t2i
return emp2.real, t2
def solve_mo1_fc(sscobj, h1):
cput1 = (time.clock(), time.time())
log = logger.Logger(sscobj.stdout, sscobj.verbose)
mol = sscobj.mol
mo_energy = sscobj._scf.mo_energy
mo_coeff = sscobj._scf.mo_coeff
mo_occ = sscobj._scf.mo_occ
nset = len(h1)
eai = 1. / lib.direct_sum('a-i->ai', mo_energy[mo_occ == 0],
mo_energy[mo_occ > 0])
mo1 = numpy.asarray(h1) * -eai
if not sscobj.cphf:
return mo1
orbo = mo_coeff[:, mo_occ > 0]
orbv = mo_coeff[:, mo_occ == 0]
nocc = orbo.shape[1]
nvir = orbv.shape[1]
nmo = nocc + nvir
vresp = _gen_rhf_response(mf, singlet=False, hermi=1)
mo_v_o = numpy.asarray(numpy.hstack((orbv, orbo)), order='F')
def vind(mo1):
dm1 = _dm1_mo2ao(mo1.reshape(nset, nvir, nocc), orbv,
orbo * 2) # *2 for double occupancy
dm1 = dm1 + dm1.transpose(0, 2, 1)
v1 = vresp(dm1)
v1 = _ao2mo.nr_e2(v1, mo_v_o,
(0, nvir, nvir, nmo)).reshape(nset, nvir, nocc)
v1 *= eai
return v1.ravel()
mo1 = lib.krylov(vind, mo1.ravel(), tol=1e-9, max_cycle=20, verbose=log)
log.timer('solving FC CPHF eqn', *cput1)
return mo1.reshape(nset, nvir, nocc)
def solve_mo1(self, mo_energy=None, mo_occ=None, h1=None, with_cphf=None):
cput1 = (time.clock(), time.time())
log = logger.Logger(self.stdout, self.verbose)
if mo_energy is None: mo_energy = self._scf.mo_energy
if mo_occ is None: mo_occ = self._scf.mo_occ
if with_cphf is None: with_cphf = self.cphf
mol = self.mol
mo_coeff = self._scf.mo_coeff
if h1 is None:
atmlst = sorted(set([j for i,j in self.nuc_pair]))
h1 = numpy.asarray(make_h1_pso(mol, mo_coeff, mo_occ, atmlst))
if with_cphf:
vind = self.gen_vind(self._scf, mo_coeff, mo_occ)
mo1, mo_e1 = cphf.solve(vind, mo_energy, mo_occ, h1, None,
self.max_cycle_cphf, self.conv_tol,
verbose=log)
else:
e_ai = lib.direct_sum('i-a->ai', mo_energy[mo_occ>0], mo_energy[mo_occ==0])
mo1 = h1 * (1 / e_ai)
mo_e1 = None
logger.timer(self, 'solving mo1 eqn', *cput1)
return mo1, mo_e1
def update_amps(mycc, t1, t2, eris):
"""
Update GCCD amplitudes.
"""
time0 = logger.process_clock(), logger.perf_counter()
log = logger.Logger(mycc.stdout, mycc.verbose)
t1T = t1.T
t2T = np.asarray(t2.transpose(2, 3, 0, 1), order='C')
nvir_seg, nvir, nocc = t2T.shape[:3]
t2 = None
ntasks = mpi.pool.size
vlocs = [_task_location(nvir, task_id) for task_id in range(ntasks)]
vloc0, vloc1 = vlocs[rank]
log.debug2('vlocs %s', vlocs)
assert vloc1 - vloc0 == nvir_seg
fock = eris.fock
fvo = fock[nocc:, :nocc]
mo_e_o = eris.mo_energy[:nocc]
mo_e_v = eris.mo_energy[nocc:] + mycc.level_shift
tauT_tilde = make_tauT(t1T, t2T, fac=0.5, vlocs=vlocs)
Fvv = cc_Fvv(t1T, t2T, eris, tauT_tilde=tauT_tilde, vlocs=vlocs)
Foo = cc_Foo(t1T, t2T, eris, tauT_tilde=tauT_tilde, vlocs=vlocs)
tauT_tilde = None
Fov = cc_Fov(t1T, eris, vlocs=vlocs)
# Move energy terms to the other side
Fvv[np.diag_indices(nvir)] -= mo_e_v
Foo[np.diag_indices(nocc)] -= mo_e_o
# T1 equation
t1Tnew = np.zeros_like(t1T)
#t1Tnew = np.dot(Fvv, t1T)
#t1Tnew -= np.dot(t1T, Foo)
tmp = einsum('aeim, me -> ai', t2T, Fov)
#tmp -= np.einsum('fn, naif -> ai', t1T, eris.oxov, optimize=True)
tmp = mpi.allgather(tmp)
#tmp2 = einsum('eamn, mnie -> ai', t2T, eris.ooox)
tmp2 = einsum('eamn, einm -> ai', t2T, eris.xooo)
#tmp2 += einsum('efim, mafe -> ai', t2T, eris.ovvx)
tmp2 += einsum('efim, efam -> ai', t2T, eris.xvvo)
tmp2 *= 0.5
tmp2 = mpi.allreduce_inplace(tmp2)
tmp += tmp2
tmp2 = None
#t1Tnew += tmp
#t1Tnew += fvo
# T2 equation
Ftmp = Fvv #- 0.5 * np.dot(t1T, Fov)
t2Tnew = einsum('aeij, be -> abij', t2T, Ftmp)
t2T_tmp = mpi.alltoall_new([t2Tnew[:, p0:p1] for p0, p1 in vlocs],
split_recvbuf=True)
for task_id, (p0, p1) in enumerate(vlocs):
tmp = t2T_tmp[task_id].reshape(p1 - p0, nvir_seg, nocc, nocc)
t2Tnew[:, p0:p1] -= tmp.transpose(1, 0, 2, 3)
tmp = None
t2T_tmp = None
Ftmp = Foo #+ 0.5 * np.dot(Fov, t1T)
tmp = einsum('abim, mj -> abij', t2T, Ftmp)
t2Tnew -= tmp
t2Tnew += tmp.transpose(0, 1, 3, 2)
tmp = None
t2Tnew += np.asarray(eris.xvoo)
tauT = make_tauT(t1T, t2T, vlocs=vlocs)
Woooo = cc_Woooo(t1T, t2T, eris, tauT=tauT, vlocs=vlocs)
Woooo *= 0.5
t2Tnew += einsum('abmn, mnij -> abij', tauT, Woooo)
Woooo = None
Wvvvv = cc_Wvvvv(t1T, t2T, eris, tauT=tauT, vlocs=vlocs)
for task_id, tauT_tmp, p0, p1 in _rotate_vir_block(tauT, vlocs=vlocs):
tmp = einsum('abef, efij -> abij', Wvvvv[:, :, p0:p1], tauT_tmp)
tmp *= 0.5
t2Tnew += tmp
tmp = tauT_tmp = None
Wvvvv = None
tauT = None
#tmp = einsum('mbje, ei -> bmij', eris.oxov, t1T) # [b]mij
#tmp = mpi.allgather(tmp) # bmij
#tmp = einsum('am, bmij -> abij', t1T[vloc0:vloc1], tmp) # [a]bij
tmp = 0.0
Wvovo = cc_Wovvo(t1T, t2T, eris, vlocs=vlocs).transpose(2, 0, 1, 3)
for task_id, w_tmp, p0, p1 in _rotate_vir_block(Wvovo, vlocs=vlocs):
tmp += einsum('aeim, embj -> abij', t2T[:, p0:p1], w_tmp)
w_tmp = None
Wvovo = None
tmp = tmp - tmp.transpose(0, 1, 3, 2)
t2Tnew += tmp
tmpT = mpi.alltoall_new([tmp[:, p0:p1] for p0, p1 in vlocs],
split_recvbuf=True)
for task_id, (p0, p1) in enumerate(vlocs):
tmp = tmpT[task_id].reshape(p1 - p0, nvir_seg, nocc, nocc)
t2Tnew[:, p0:p1] -= tmp.transpose(1, 0, 2, 3)
tmp = None
tmpT = None
#tmp = einsum('ei, jeba -> abij', t1T, eris.ovvx)
#t2Tnew += tmp
#t2Tnew -= tmp.transpose(0, 1, 3, 2)
#tmp = einsum('am, ijmb -> baij', t1T, eris.ooox.conj())
#t2Tnew += tmp
#tmpT = mpi.alltoall([tmp[:, p0:p1] for p0, p1 in vlocs],
# split_recvbuf=True)
#for task_id, (p0, p1) in enumerate(vlocs):
# tmp = tmpT[task_id].reshape(p1-p0, nvir_seg, nocc, nocc)
# t2Tnew[:, p0:p1] -= tmp.transpose(1, 0, 2, 3)
# tmp = None
#tmpT = None
eia = mo_e_o[:, None] - mo_e_v
#t1Tnew /= eia.T
for i in range(vloc0, vloc1):
t2Tnew[i - vloc0] /= lib.direct_sum('i + jb -> bij', eia[:, i], eia)
time0 = log.timer_debug1('update t1 t2', *time0)
return t1Tnew.T, t2Tnew.transpose(2, 3, 0, 1)
def kernel(mycc,
t1=None,
t2=None,
l1=None,
l2=None,
eris=None,
atmlst=None,
mf_grad=None,
verbose=logger.INFO):
if t1 is None: t1 = mycc.t1
if t2 is None: t2 = mycc.t2
if l1 is None: l1 = mycc.l1
if l2 is None: l2 = mycc.l2
if eris is None: eris = ccsd._ERIS(mycc)
if mf_grad is None:
mf_grad = rhf_grad.Gradients(mycc._scf)
log = logger.Logger(mycc.stdout, mycc.verbose)
time0 = time.clock(), time.time()
mol = mycc.mol
moidx = numpy.ones(mycc.mo_coeff.shape[1], dtype=numpy.bool)
if isinstance(mycc.frozen, (int, numpy.integer)):
raise NotImplementedError('frozen orbital ccsd_grad')
moidx[:mycc.frozen] = False
else:
moidx[mycc.frozen] = False
mo_coeff = mycc.mo_coeff[:,
moidx] #FIXME: ensure mycc.mo_coeff is canonical orbital
mo_energy = eris.fock.diagonal()
nocc, nvir = t1.shape
nao, nmo = mo_coeff.shape
nao_pair = nao * (nao + 1) // 2
log.debug('Build ccsd rdm1 intermediates')
d1 = ccsd_rdm.gamma1_intermediates(mycc, t1, t2, l1, l2)
doo, dov, dvo, dvv = d1
time1 = log.timer('rdm1 intermediates', *time0)
log.debug('Build ccsd rdm2 intermediates')
_d2tmpfile = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
fd2intermediate = h5py.File(_d2tmpfile.name, 'w')
d2 = ccsd_rdm.gamma2_outcore(mycc, t1, t2, l1, l2, fd2intermediate)
time1 = log.timer('rdm2 intermediates', *time1)
log.debug('Build ccsd response_rdm1')
Ioo, Ivv, Ivo, Xvo = IX_intermediates(mycc, t1, t2, l1, l2, eris, d1, d2)
time1 = log.timer('response_rdm1 intermediates', *time1)
dm1mo = response_dm1(mycc, t1, t2, l1, l2, eris, (Ioo, Ivv, Ivo, Xvo))
dm1mo[:nocc, :nocc] = doo + doo.T
dm1mo[nocc:, nocc:] = dvv + dvv.T
dm1ao = reduce(numpy.dot, (mo_coeff, dm1mo, mo_coeff.T))
im1 = numpy.zeros_like(dm1mo)
im1[:nocc, :nocc] = Ioo
im1[nocc:, nocc:] = Ivv
im1[nocc:, :nocc] = Ivo
im1[:nocc, nocc:] = Ivo.T
im1 = reduce(numpy.dot, (mo_coeff, im1, mo_coeff.T))
time1 = log.timer('response_rdm1', *time1)
log.debug('symmetrized rdm2 and MO->AO transformation')
_dm2file = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
# Basically, 4 times of dm2 is computed. *2 in _rdm2_mo2ao, *2 in _load_block_tril
fdm2 = h5py.File(_dm2file.name, 'w')
dm1_with_hf = dm1mo.copy()
for i in range(
nocc
): # HF 2pdm ~ 4(ij)(kl)-2(il)(jk), diagonal+1 because of 4*dm2
dm1_with_hf[i, i] += 1
_rdm2_mo2ao(mycc, d2, dm1_with_hf, mo_coeff, fdm2)
time1 = log.timer('MO->AO transformation', *time1)
for key in fd2intermediate.keys():
del (fd2intermediate[key])
fd2intermediate.close()
#TODO: pass hf_grad object to compute h1 and s1
log.debug('h1 and JK1')
h1 = mf_grad.get_hcore(mol)
s1 = mf_grad.get_ovlp(mol)
zeta = lib.direct_sum('i+j->ij', mo_energy, mo_energy) * .5
zeta[nocc:, :nocc] = mo_energy[:nocc]
zeta[:nocc, nocc:] = mo_energy[:nocc].reshape(-1, 1)
zeta = reduce(numpy.dot, (mo_coeff, zeta * dm1mo, mo_coeff.T))
p1 = numpy.dot(mo_coeff[:, :nocc], mo_coeff[:, :nocc].T)
vhf4sij = reduce(numpy.dot,
(p1, mycc._scf.get_veff(mol, dm1ao + dm1ao.T), p1))
time1 = log.timer('h1 and JK1', *time1)
# Hartree-Fock part contribution
hf_dm1 = mycc._scf.make_rdm1(mycc._scf.mo_coeff, mycc._scf.mo_occ)
dm1ao += hf_dm1
zeta += mf_grad.make_rdm1e(mycc._scf.mo_energy, mycc._scf.mo_coeff,
mycc._scf.mo_occ)
if atmlst is None:
atmlst = range(mol.natm)
offsetdic = mol.offset_nr_by_atom()
max_memory = mycc.max_memory - lib.current_memory()[0]
blksize = max(1, int(max_memory * 1e6 / 8 / (nao**3 * 2.5)))
ioblksize = fdm2['dm2/0'].shape[-1]
de = numpy.zeros((len(atmlst), 3))
for k, ia in enumerate(atmlst):
shl0, shl1, p0, p1 = offsetdic[ia]
# s[1] dot I, note matrix im1 is not hermitian
de[k] = (numpy.einsum('xij,ij->x', s1[:, p0:p1], im1[p0:p1]) +
numpy.einsum('xji,ij->x', s1[:, p0:p1], im1[:, p0:p1]))
# h[1] \dot DM, *2 for +c.c., contribute to f1
h1ao = mf_grad._grad_rinv(mol, ia)
h1ao[:, p0:p1] += h1[:, p0:p1]
de[k] += (numpy.einsum('xij,ij->x', h1ao, dm1ao) +
numpy.einsum('xji,ij->x', h1ao, dm1ao))
# -s[1]*e \dot DM, contribute to f1
de[k] -= (numpy.einsum('xij,ij->x', s1[:, p0:p1], zeta[p0:p1]) +
numpy.einsum('xji,ij->x', s1[:, p0:p1], zeta[:, p0:p1]))
# -vhf[s_ij[1]], contribute to f1, *2 for s1+s1.T
de[k] -= numpy.einsum('xij,ij->x', s1[:, p0:p1], vhf4sij[p0:p1]) * 2
# 2e AO integrals dot 2pdm
ip0 = p0
for b0, b1, nf in shell_prange(mol, shl0, shl1, blksize):
eri1 = mol.intor('cint2e_ip1_sph',
comp=3,
aosym='s2kl',
shls_slice=(b0, b1, 0, mol.nbas, 0, mol.nbas, 0,
mol.nbas))
eri1 = eri1.reshape(3, nf, nao, -1)
dm2buf = numpy.empty((nf, nao, nao_pair))
for ic, (i0, i1) in enumerate(prange(0, nao_pair, ioblksize)):
_load_block_tril(fdm2['dm2/%d' % ic], ip0, ip0 + nf,
dm2buf[:, :, i0:i1])
de[k] -= numpy.einsum('xijk,ijk->x', eri1, dm2buf) * 2
eri1 = dm2buf = None
ip0 += nf
log.debug('grad of atom %d %s = %s', ia, mol.atom_symbol(ia), de[k])
time1 = log.timer('grad of atom %d' % ia, *time1)
log.note('CCSD gradinets')
log.note('==============')
log.note(' x y z')
for k, ia in enumerate(atmlst):
log.note('%d %s %15.9f %15.9f %15.9f', ia, mol.atom_symbol(ia),
de[k, 0], de[k, 1], de[k, 2])
log.timer('CCSD gradients', *time0)
for key in fdm2.keys():
del (fdm2[key])
fdm2.close()
_d2tmpfile = _dm2file = None
return de
eri_mo = ao2mo.kernel(mf._eri, mf.mo_coeff, compact=False)
nmo = mf.mo_coeff.shape[1]
eri_mo = eri_mo.reshape(nmo, nmo, nmo, nmo)
dm1 = make_rdm1(mcc, t1, t2, l1, l2, eris=eris)
dm2 = make_rdm2(mcc, t1, t2, l1, l2, eris=eris)
h1 = reduce(numpy.dot, (mf.mo_coeff.T, mf.get_hcore(), mf.mo_coeff))
e3 = (numpy.einsum('ij,ij->', h1, dm1) +
numpy.einsum('ijkl,ijkl->', eri_mo, dm2) * .5 + mf.mol.energy_nuc())
#print e3ref, e3-(mf.e_tot+ecc)
nocc, nvir = t1.shape
eris_ovvv = _cp(eris.ovvv)
eris_ovvv = lib.unpack_tril(eris_ovvv.reshape(nocc * nvir, -1))
eris_ovvv = eris_ovvv.reshape(nocc, nvir, nvir, nvir)
mo_e = mcc._scf.mo_energy
eia = lib.direct_sum('i-a->ia', mo_e[:nocc], mo_e[nocc:])
d3 = lib.direct_sum('ia,jb,kc->ijkabc', eia, eia, eia)
eris_ovoo = eris.ovoo
w = (numpy.einsum('iabf,kjcf->ijkabc', eris_ovvv, t2) -
numpy.einsum('iajm,mkbc->ijkabc', eris_ovoo, t2)) / d3
v = numpy.einsum('iajb,kc->ijkabc', eris.ovov, t1) / d3 * .5
w = ccsd_t.p6_(w)
v = ccsd_t.p6_(v)
rw = ccsd_t.r6_(w)
rwv = ccsd_t.r6_(w * 2 + v * 0)
dovov = numpy.einsum('kc,ijkabc->iajb', t1, rw)
dooov = -numpy.einsum('mkbc,ijkabc->jmia', t2, rwv)
dovvv = numpy.einsum('kjcf,ijkabc->iabf', t2, rwv)
e3a = numpy.einsum('iajb,iajb', eris.ovov, dovov)
e3a += numpy.einsum('iajm,jmia', eris.ovoo, dooov)
e3a += numpy.einsum('iabf,iabf', eris_ovvv, dovvv)
def kernel(mcc, eris, t1=None, t2=None):
if t1 is None or t2 is None:
t1, t2 = mcc.t1, mcc.t2
def p6(t):
return (t + t.transpose(1,2,0,4,5,3) +
t.transpose(2,0,1,5,3,4) + t.transpose(0,2,1,3,5,4) +
t.transpose(2,1,0,5,4,3) + t.transpose(1,0,2,4,3,5))
def r6(w):
return (w + w.transpose(2,0,1,3,4,5) + w.transpose(1,2,0,3,4,5)
- w.transpose(2,1,0,3,4,5) - w.transpose(0,2,1,3,4,5)
- w.transpose(1,0,2,3,4,5))
t1a, t1b = t1
t2aa, t2ab, t2bb = t2
nocca, noccb = t2ab.shape[:2]
mo_ea, mo_eb = eris.mo_energy
eia = mo_ea[:nocca,None] - mo_ea[nocca:]
eIA = mo_eb[:noccb,None] - mo_eb[noccb:]
fvo = eris.focka[nocca:,:nocca]
fVO = eris.fockb[noccb:,:noccb]
# aaa
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eia, eia, eia)
w = numpy.einsum('ijae,kceb->ijkabc', t2aa, numpy.asarray(eris.get_ovvv()).conj())
w-= numpy.einsum('mkbc,iajm->ijkabc', t2aa, numpy.asarray(eris.ovoo.conj()))
r = r6(w)
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.ovov).conj(), t1a)
v+= numpy.einsum('jkbc,ai->ijkabc', t2aa, fvo) * .5
wvd = p6(w + v) / d3
et = numpy.einsum('ijkabc,ijkabc', wvd.conj(), r)
# bbb
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eIA, eIA, eIA)
w = numpy.einsum('ijae,kceb->ijkabc', t2bb, numpy.asarray(eris.get_OVVV()).conj())
w-= numpy.einsum('imab,kcjm->ijkabc', t2bb, numpy.asarray(eris.OVOO.conj()))
r = r6(w)
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.OVOV).conj(), t1b)
v+= numpy.einsum('jkbc,ai->ijkabc', t2bb, fVO) * .5
wvd = p6(w + v) / d3
et += numpy.einsum('ijkabc,ijkabc', wvd.conj(), r)
# baa
w = numpy.einsum('jIeA,kceb->IjkAbc', t2ab, numpy.asarray(eris.get_ovvv()).conj()) * 2
w += numpy.einsum('jIbE,kcEA->IjkAbc', t2ab, numpy.asarray(eris.get_ovVV()).conj()) * 2
w += numpy.einsum('jkbe,IAec->IjkAbc', t2aa, numpy.asarray(eris.get_OVvv()).conj())
w -= numpy.einsum('mIbA,kcjm->IjkAbc', t2ab, numpy.asarray(eris.ovoo).conj()) * 2
w -= numpy.einsum('jMbA,kcIM->IjkAbc', t2ab, numpy.asarray(eris.ovOO).conj()) * 2
w -= numpy.einsum('jmbc,IAkm->IjkAbc', t2aa, numpy.asarray(eris.OVoo).conj())
r = w - w.transpose(0,2,1,3,4,5)
r = r + r.transpose(0,2,1,3,5,4)
v = numpy.einsum('jbkc,IA->IjkAbc', numpy.asarray(eris.ovov).conj(), t1b)
v += numpy.einsum('kcIA,jb->IjkAbc', numpy.asarray(eris.ovOV).conj(), t1a)
v += numpy.einsum('kcIA,jb->IjkAbc', numpy.asarray(eris.ovOV).conj(), t1a)
v += numpy.einsum('jkbc,AI->IjkAbc', t2aa, fVO) * .5
v += numpy.einsum('kIcA,bj->IjkAbc', t2ab, fvo) * 2
w += v
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eIA, eia, eia)
r /= d3
et += numpy.einsum('ijkabc,ijkabc', w.conj(), r)
# bba
w = numpy.einsum('ijae,kceb->ijkabc', t2ab, numpy.asarray(eris.get_OVVV()).conj()) * 2
w += numpy.einsum('ijeb,kcea->ijkabc', t2ab, numpy.asarray(eris.get_OVvv()).conj()) * 2
w += numpy.einsum('jkbe,iaec->ijkabc', t2bb, numpy.asarray(eris.get_ovVV()).conj())
w -= numpy.einsum('imab,kcjm->ijkabc', t2ab, numpy.asarray(eris.OVOO).conj()) * 2
w -= numpy.einsum('mjab,kcim->ijkabc', t2ab, numpy.asarray(eris.OVoo).conj()) * 2
w -= numpy.einsum('jmbc,iakm->ijkabc', t2bb, numpy.asarray(eris.ovOO).conj())
r = w - w.transpose(0,2,1,3,4,5)
r = r + r.transpose(0,2,1,3,5,4)
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.OVOV).conj(), t1a)
v += numpy.einsum('iakc,jb->ijkabc', numpy.asarray(eris.ovOV).conj(), t1b)
v += numpy.einsum('iakc,jb->ijkabc', numpy.asarray(eris.ovOV).conj(), t1b)
v += numpy.einsum('JKBC,ai->iJKaBC', t2bb, fvo) * .5
v += numpy.einsum('iKaC,BJ->iJKaBC', t2ab, fVO) * 2
w += v
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eia, eIA, eIA)
r /= d3
et += numpy.einsum('ijkabc,ijkabc', w.conj(), r)
et *= .25
return et
def update_amps(cc, t1, t2, eris):
time0 = time.clock(), time.time()
log = logger.Logger(cc.stdout, cc.verbose)
nocc, nvir = t1.shape
fock = eris.fock
fov = fock[:nocc,nocc:]
foo = fock[:nocc,:nocc]
fvv = fock[nocc:,nocc:]
mo_e = eris.fock.diagonal()
eia = mo_e[:nocc,None] - mo_e[None,nocc:]
eijab = lib.direct_sum('ia,jb->ijab',eia,eia)
tau = imd.make_tau(t2,t1,t1)
Fvv = imd.cc_Fvv(t1,t2,eris)
Foo = imd.cc_Foo(t1,t2,eris)
Fov = imd.cc_Fov(t1,t2,eris)
Woooo = imd.cc_Woooo(t1,t2,eris)
Wvvvv = imd.cc_Wvvvv(t1,t2,eris)
Wovvo = imd.cc_Wovvo(t1,t2,eris)
# Move energy terms to the other side
Fvv -= np.diag(np.diag(fvv))
Foo -= np.diag(np.diag(foo))
# T1 equation
t1new = np.array(fov).conj()
t1new += einsum('ie,ae->ia',t1,Fvv)
t1new += -einsum('ma,mi->ia',t1,Foo)
t1new += einsum('imae,me->ia',t2,Fov)
t1new += -einsum('nf,naif->ia',t1,eris.ovov)
t1new += -0.5*einsum('imef,maef->ia',t2,eris.ovvv)
t1new += -0.5*einsum('mnae,mnie->ia',t2,eris.ooov)
# T2 equation
t2new = np.array(eris.oovv).conj()
Ftmp = Fvv - 0.5*einsum('mb,me->be',t1,Fov)
tmp = einsum('ijae,be->ijab',t2,Ftmp)
t2new += (tmp - tmp.transpose(0,1,3,2))
Ftmp = Foo + 0.5*einsum('je,me->mj',t1,Fov)
tmp = einsum('imab,mj->ijab',t2,Ftmp)
t2new -= (tmp - tmp.transpose(1,0,2,3))
t2new += 0.5*einsum('mnab,mnij->ijab',tau,Woooo)
for a in range(nvir):
t2new[:,:,a,:] += 0.5*einsum('ijef,bef->ijb',tau,Wvvvv[a])
tmp = einsum('imae,mbej->ijab',t2,Wovvo)
tmp -= -einsum('ie,ma,mbje->ijab',t1,t1,eris.ovov)
t2new += ( tmp - tmp.transpose(0,1,3,2)
- tmp.transpose(1,0,2,3) + tmp.transpose(1,0,3,2) )
tmp = einsum('ie,jeba->ijab',t1,np.array(eris.ovvv).conj())
t2new += (tmp - tmp.transpose(1,0,2,3))
tmp = einsum('ma,mbij->ijab',t1,eris.ovoo)
t2new -= (tmp - tmp.transpose(0,1,3,2))
t1new /= eia
t2new /= eijab
time0 = log.timer_debug1('update t1 t2', *time0)
return t1new, t2new
def kernel(mycc,
t1=None,
t2=None,
l1=None,
l2=None,
eris=None,
atmlst=None,
mf_grad=None,
d1=None,
d2=None,
verbose=logger.INFO):
if eris is not None:
if abs(eris.fock - numpy.diag(eris.fock.diagonal())).max() > 1e-3:
raise RuntimeError(
'CCSD gradients does not support NHF (non-canonical HF)')
if t1 is None: t1 = mycc.t1
if t2 is None: t2 = mycc.t2
if l1 is None: l1 = mycc.l1
if l2 is None: l2 = mycc.l2
if mf_grad is None: mf_grad = mycc._scf.nuc_grad_method()
log = logger.new_logger(mycc, verbose)
time0 = time.clock(), time.time()
log.debug('Build ccsd rdm1 intermediates')
if d1 is None:
d1 = ccsd_rdm._gamma1_intermediates(mycc, t1, t2, l1, l2)
doo, dov, dvo, dvv = d1
time1 = log.timer_debug1('rdm1 intermediates', *time0)
log.debug('Build ccsd rdm2 intermediates')
fdm2 = lib.H5TmpFile()
if d2 is None:
d2 = ccsd_rdm._gamma2_outcore(mycc, t1, t2, l1, l2, fdm2, True)
time1 = log.timer_debug1('rdm2 intermediates', *time1)
mol = mycc.mol
mo_coeff = mycc.mo_coeff
mo_energy = mycc._scf.mo_energy
nao, nmo = mo_coeff.shape
nocc = numpy.count_nonzero(mycc.mo_occ > 0)
with_frozen = not (mycc.frozen is None or mycc.frozen is 0)
OA, VA, OF, VF = _index_frozen_active(mycc.get_frozen_mask(), mycc.mo_occ)
log.debug('symmetrized rdm2 and MO->AO transformation')
# Roughly, dm2*2 is computed in _rdm2_mo2ao
mo_active = mo_coeff[:, numpy.hstack((OA, VA))]
_rdm2_mo2ao(mycc, d2, mo_active, fdm2) # transform the active orbitals
time1 = log.timer_debug1('MO->AO transformation', *time1)
hf_dm1 = mycc._scf.make_rdm1(mycc.mo_coeff, mycc.mo_occ)
if atmlst is None:
atmlst = range(mol.natm)
offsetdic = mol.offset_nr_by_atom()
diagidx = numpy.arange(nao)
diagidx = diagidx * (diagidx + 1) // 2 + diagidx
de = numpy.zeros((len(atmlst), 3))
Imat = numpy.zeros((nao, nao))
vhf1 = fdm2.create_dataset('vhf1', (len(atmlst), 3, nao, nao), 'f8')
# 2e AO integrals dot 2pdm
max_memory = max(0, mycc.max_memory - lib.current_memory()[0])
blksize = max(1, int(max_memory * .9e6 / 8 / (nao**3 * 2.5)))
for k, ia in enumerate(atmlst):
shl0, shl1, p0, p1 = offsetdic[ia]
ip1 = p0
vhf = numpy.zeros((3, nao, nao))
for b0, b1, nf in _shell_prange(mol, shl0, shl1, blksize):
ip0, ip1 = ip1, ip1 + nf
dm2buf = _load_block_tril(fdm2['dm2'], ip0, ip1, nao)
dm2buf[:, :, diagidx] *= .5
shls_slice = (b0, b1, 0, mol.nbas, 0, mol.nbas, 0, mol.nbas)
eri0 = mol.intor('int2e', aosym='s2kl', shls_slice=shls_slice)
Imat += lib.einsum('ipx,iqx->pq', eri0.reshape(nf, nao, -1),
dm2buf)
eri0 = None
eri1 = mol.intor('int2e_ip1',
comp=3,
aosym='s2kl',
shls_slice=shls_slice).reshape(3, nf, nao, -1)
de[k] -= numpy.einsum('xijk,ijk->x', eri1, dm2buf) * 2
dm2buf = None
# HF part
for i in range(3):
eri1tmp = lib.unpack_tril(eri1[i].reshape(nf * nao, -1))
eri1tmp = eri1tmp.reshape(nf, nao, nao, nao)
vhf[i] += numpy.einsum('ijkl,ij->kl', eri1tmp, hf_dm1[ip0:ip1])
vhf[i] -= numpy.einsum('ijkl,il->kj', eri1tmp,
hf_dm1[ip0:ip1]) * .5
vhf[i, ip0:ip1] += numpy.einsum('ijkl,kl->ij', eri1tmp, hf_dm1)
vhf[i, ip0:ip1] -= numpy.einsum('ijkl,jk->il', eri1tmp,
hf_dm1) * .5
eri1 = eri1tmp = None
vhf1[k] = vhf
log.debug('2e-part grad of atom %d %s = %s', ia, mol.atom_symbol(ia),
de[k])
time1 = log.timer_debug1('2e-part grad of atom %d' % ia, *time1)
Imat = reduce(numpy.dot,
(mo_coeff.T, Imat, mycc._scf.get_ovlp(), mo_coeff)) * -1
dm1mo = numpy.zeros((nmo, nmo))
if with_frozen:
dco = Imat[OF[:, None], OA] / (mo_energy[OF, None] - mo_energy[OA])
dfv = Imat[VF[:, None], VA] / (mo_energy[VF, None] - mo_energy[VA])
dm1mo[OA[:, None], OA] = doo + doo.T
dm1mo[OF[:, None], OA] = dco
dm1mo[OA[:, None], OF] = dco.T
dm1mo[VA[:, None], VA] = dvv + dvv.T
dm1mo[VF[:, None], VA] = dfv
dm1mo[VA[:, None], VF] = dfv.T
else:
dm1mo[:nocc, :nocc] = doo + doo.T
dm1mo[nocc:, nocc:] = dvv + dvv.T
dm1 = reduce(numpy.dot, (mo_coeff, dm1mo, mo_coeff.T))
vhf = mycc._scf.get_veff(mycc.mol, dm1) * 2
Xvo = reduce(numpy.dot, (mo_coeff[:, nocc:].T, vhf, mo_coeff[:, :nocc]))
Xvo += Imat[:nocc, nocc:].T - Imat[nocc:, :nocc]
dm1mo += _response_dm1(mycc, Xvo, eris)
time1 = log.timer_debug1('response_rdm1 intermediates', *time1)
Imat[nocc:, :nocc] = Imat[:nocc, nocc:].T
im1 = reduce(numpy.dot, (mo_coeff, Imat, mo_coeff.T))
time1 = log.timer_debug1('response_rdm1', *time1)
log.debug('h1 and JK1')
hcore_deriv = mf_grad.hcore_generator(mol)
s1 = mf_grad.get_ovlp(mol)
zeta = lib.direct_sum('i+j->ij', mo_energy, mo_energy) * .5
zeta[nocc:, :nocc] = mo_energy[:nocc]
zeta[:nocc, nocc:] = mo_energy[:nocc].reshape(-1, 1)
zeta = reduce(numpy.dot, (mo_coeff, zeta * dm1mo, mo_coeff.T))
dm1 = reduce(numpy.dot, (mo_coeff, dm1mo, mo_coeff.T))
p1 = numpy.dot(mo_coeff[:, :nocc], mo_coeff[:, :nocc].T)
vhf_s1occ = reduce(numpy.dot,
(p1, mycc._scf.get_veff(mol, dm1 + dm1.T), p1))
time1 = log.timer_debug1('h1 and JK1', *time1)
# Hartree-Fock part contribution
dm1p = hf_dm1 + dm1 * 2
dm1 += hf_dm1
zeta += mf_grad.make_rdm1e(mo_energy, mo_coeff, mycc.mo_occ)
for k, ia in enumerate(atmlst):
shl0, shl1, p0, p1 = offsetdic[ia]
# s[1] dot I, note matrix im1 is not hermitian
de[k] += numpy.einsum('xij,ij->x', s1[:, p0:p1], im1[p0:p1])
de[k] += numpy.einsum('xji,ij->x', s1[:, p0:p1], im1[:, p0:p1])
# h[1] \dot DM, contribute to f1
h1ao = hcore_deriv(ia)
de[k] += numpy.einsum('xij,ji->x', h1ao, dm1)
# -s[1]*e \dot DM, contribute to f1
de[k] -= numpy.einsum('xij,ij->x', s1[:, p0:p1], zeta[p0:p1])
de[k] -= numpy.einsum('xji,ij->x', s1[:, p0:p1], zeta[:, p0:p1])
# -vhf[s_ij[1]], contribute to f1, *2 for s1+s1.T
de[k] -= numpy.einsum('xij,ij->x', s1[:, p0:p1], vhf_s1occ[p0:p1]) * 2
de[k] -= numpy.einsum('xij,ij->x', vhf1[k], dm1p)
de += mf_grad.grad_nuc(mol, atmlst)
log.timer('%s gradients' % mycc.__class__.__name__, *time0)
return de
def update_amps(cc, t1, t2, eris):
# Ref: Hirata et al., J. Chem. Phys. 120, 2581 (2004) Eqs.(35)-(36)
nocc, nvir = t1.shape
fock = eris.fock
fov = fock[:nocc, nocc:].copy()
foo = fock[:nocc, :nocc].copy()
fvv = fock[nocc:, nocc:].copy()
Foo = imd.cc_Foo(t1, t2, eris)
Fvv = imd.cc_Fvv(t1, t2, eris)
Fov = imd.cc_Fov(t1, t2, eris)
# Move energy terms to the other side
Foo -= np.diag(np.diag(foo))
Fvv -= np.diag(np.diag(fvv))
# T1 equation
t1new = np.asarray(fov).conj().copy()
t1new += -2 * einsum('kc,ka,ic->ia', fov, t1, t1)
t1new += einsum('ac,ic->ia', Fvv, t1)
t1new += -einsum('ki,ka->ia', Foo, t1)
t1new += 2 * einsum('kc,kica->ia', Fov, t2)
t1new += -einsum('kc,ikca->ia', Fov, t2)
t1new += einsum('kc,ic,ka->ia', Fov, t1, t1)
t1new += 2 * einsum('kcai,kc->ia', eris.ovvo, t1)
t1new += -einsum('kiac,kc->ia', eris.oovv, t1)
eris_ovvv = np.asarray(eris.ovvv)
t1new += 2 * einsum('kdac,ikcd->ia', eris_ovvv, t2)
t1new += -einsum('kcad,ikcd->ia', eris_ovvv, t2)
t1new += 2 * einsum('kdac,kd,ic->ia', eris_ovvv, t1, t1)
t1new += -einsum('kcad,kd,ic->ia', eris_ovvv, t1, t1)
t1new += -2 * einsum('kilc,klac->ia', eris.ooov, t2)
t1new += einsum('likc,klac->ia', eris.ooov, t2)
t1new += -2 * einsum('kilc,lc,ka->ia', eris.ooov, t1, t1)
t1new += einsum('likc,lc,ka->ia', eris.ooov, t1, t1)
# T2 equation
t2new = np.asarray(eris.ovov).conj().transpose(0, 2, 1, 3).copy()
if cc.cc2:
Woooo2 = np.asarray(eris.oooo).transpose(0, 2, 1, 3).copy()
Woooo2 += einsum('kilc,jc->klij', eris.ooov, t1)
Woooo2 += einsum('ljkc,ic->klij', eris.ooov, t1)
Woooo2 += einsum('kcld,ic,jd->klij', eris.ovov, t1, t1)
t2new += einsum('klij,ka,lb->ijab', Woooo2, t1, t1)
Wvvvv = einsum('kcbd,ka->abcd', eris_ovvv, -t1)
Wvvvv = Wvvvv + Wvvvv.transpose(1, 0, 3, 2)
Wvvvv += np.asarray(eris.vvvv).transpose(0, 2, 1, 3)
t2new += einsum('abcd,ic,jd->ijab', Wvvvv, t1, t1)
Lvv2 = fvv - einsum('kc,ka->ac', fov, t1)
Lvv2 -= np.diag(np.diag(fvv))
tmp = einsum('ac,ijcb->ijab', Lvv2, t2)
t2new += (tmp + tmp.transpose(1, 0, 3, 2))
Loo2 = foo + einsum('kc,ic->ki', fov, t1)
Loo2 -= np.diag(np.diag(foo))
tmp = einsum('ki,kjab->ijab', Loo2, t2)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
else:
Loo = imd.Loo(t1, t2, eris)
Lvv = imd.Lvv(t1, t2, eris)
Loo -= np.diag(np.diag(foo))
Lvv -= np.diag(np.diag(fvv))
Woooo = imd.cc_Woooo(t1, t2, eris)
Wvoov = imd.cc_Wvoov(t1, t2, eris)
Wvovo = imd.cc_Wvovo(t1, t2, eris)
Wvvvv = imd.cc_Wvvvv(t1, t2, eris)
tau = t2 + einsum('ia,jb->ijab', t1, t1)
t2new += einsum('klij,klab->ijab', Woooo, tau)
t2new += einsum('abcd,ijcd->ijab', Wvvvv, tau)
tmp = einsum('ac,ijcb->ijab', Lvv, t2)
t2new += (tmp + tmp.transpose(1, 0, 3, 2))
tmp = einsum('ki,kjab->ijab', Loo, t2)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
tmp = 2 * einsum('akic,kjcb->ijab', Wvoov, t2)
tmp -= einsum('akci,kjcb->ijab', Wvovo, t2)
t2new += (tmp + tmp.transpose(1, 0, 3, 2))
tmp = einsum('akic,kjbc->ijab', Wvoov, t2)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
tmp = einsum('bkci,kjac->ijab', Wvovo, t2)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
tmp2 = einsum('kibc,ka->abic', eris.oovv, -t1)
tmp2 += np.asarray(eris.ovvv).conj().transpose(1, 3, 0, 2)
tmp = einsum('abic,jc->ijab', tmp2, t1)
t2new += (tmp + tmp.transpose(1, 0, 3, 2))
tmp2 = einsum('kcai,jc->akij', eris.ovvo, t1)
tmp2 += np.asarray(eris.ooov).transpose(3, 1, 2, 0).conj()
tmp = einsum('akij,kb->ijab', tmp2, t1)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
mo_e = eris.fock.diagonal().real
eia = mo_e[:nocc, None] - mo_e[None, nocc:]
eijab = lib.direct_sum('ia,jb->ijab', eia, eia)
t1new /= eia
t2new /= eijab
return t1new, t2new
def grad_elec(mp_grad, t2, atmlst=None, verbose=logger.INFO):
mp = mp_grad.base
log = logger.new_logger(mp, verbose)
time0 = logger.process_clock(), logger.perf_counter()
log.debug('Build mp2 rdm1 intermediates')
d1 = mp2._gamma1_intermediates(mp, t2)
doo, dvv = d1
time1 = log.timer_debug1('rdm1 intermediates', *time0)
# Set nocc, nvir for half-transformation of 2pdm. Frozen orbitals are exculded.
# nocc, nvir should be updated to include the frozen orbitals when proceeding
# the 1-particle quantities later.
mol = mp_grad.mol
with_frozen = not ((mp.frozen is None) or
(isinstance(mp.frozen,
(int, numpy.integer)) and mp.frozen == 0) or
(len(mp.frozen) == 0))
OA, VA, OF, VF = _index_frozen_active(mp.get_frozen_mask(), mp.mo_occ)
orbo = mp.mo_coeff[:, OA]
orbv = mp.mo_coeff[:, VA]
nao, nocc = orbo.shape
nvir = orbv.shape[1]
# Partially transform MP2 density matrix and hold it in memory
# The rest transformation are applied during the contraction to ERI integrals
part_dm2 = _ao2mo.nr_e2(t2.reshape(nocc**2, nvir**2),
numpy.asarray(orbv.T, order='F'), (0, nao, 0, nao),
's1', 's1').reshape(nocc, nocc, nao, nao)
part_dm2 = (part_dm2.transpose(0, 2, 3, 1) * 4 -
part_dm2.transpose(0, 3, 2, 1) * 2)
hf_dm1 = mp._scf.make_rdm1(mp.mo_coeff, mp.mo_occ)
if atmlst is None:
atmlst = range(mol.natm)
offsetdic = mol.offset_nr_by_atom()
diagidx = numpy.arange(nao)
diagidx = diagidx * (diagidx + 1) // 2 + diagidx
de = numpy.zeros((len(atmlst), 3))
Imat = numpy.zeros((nao, nao))
fdm2 = lib.H5TmpFile()
vhf1 = fdm2.create_dataset('vhf1', (len(atmlst), 3, nao, nao), 'f8')
# 2e AO integrals dot 2pdm
max_memory = max(0, mp.max_memory - lib.current_memory()[0])
blksize = max(1, int(max_memory * .9e6 / 8 / (nao**3 * 2.5)))
for k, ia in enumerate(atmlst):
shl0, shl1, p0, p1 = offsetdic[ia]
ip1 = p0
vhf = numpy.zeros((3, nao, nao))
for b0, b1, nf in _shell_prange(mol, shl0, shl1, blksize):
ip0, ip1 = ip1, ip1 + nf
dm2buf = lib.einsum('pi,iqrj->pqrj', orbo[ip0:ip1], part_dm2)
dm2buf += lib.einsum('qi,iprj->pqrj', orbo, part_dm2[:, ip0:ip1])
dm2buf = lib.einsum('pqrj,sj->pqrs', dm2buf, orbo)
dm2buf = dm2buf + dm2buf.transpose(0, 1, 3, 2)
dm2buf = lib.pack_tril(dm2buf.reshape(-1, nao,
nao)).reshape(nf, nao, -1)
dm2buf[:, :, diagidx] *= .5
shls_slice = (b0, b1, 0, mol.nbas, 0, mol.nbas, 0, mol.nbas)
eri0 = mol.intor('int2e', aosym='s2kl', shls_slice=shls_slice)
Imat += lib.einsum('ipx,iqx->pq', eri0.reshape(nf, nao, -1),
dm2buf)
eri0 = None
eri1 = mol.intor('int2e_ip1',
comp=3,
aosym='s2kl',
shls_slice=shls_slice).reshape(3, nf, nao, -1)
de[k] -= numpy.einsum('xijk,ijk->x', eri1, dm2buf) * 2
dm2buf = None
# HF part
for i in range(3):
eri1tmp = lib.unpack_tril(eri1[i]).reshape(nf * nao, -1)
eri1tmp = eri1tmp.reshape(nf, nao, nao, nao)
vhf[i] += numpy.einsum('ijkl,ij->kl', eri1tmp, hf_dm1[ip0:ip1])
vhf[i] -= numpy.einsum('ijkl,il->kj', eri1tmp,
hf_dm1[ip0:ip1]) * .5
vhf[i, ip0:ip1] += numpy.einsum('ijkl,kl->ij', eri1tmp, hf_dm1)
vhf[i, ip0:ip1] -= numpy.einsum('ijkl,jk->il', eri1tmp,
hf_dm1) * .5
eri1 = eri1tmp = None
vhf1[k] = vhf
log.debug('2e-part grad of atom %d %s = %s', ia, mol.atom_symbol(ia),
de[k])
time1 = log.timer_debug1('2e-part grad of atom %d' % ia, *time1)
# Recompute nocc, nvir to include the frozen orbitals and make contraction for
# the 1-particle quantities, see also the kernel function in ccsd_grad module.
mo_coeff = mp.mo_coeff
mo_energy = mp._scf.mo_energy
nao, nmo = mo_coeff.shape
nocc = numpy.count_nonzero(mp.mo_occ > 0)
Imat = reduce(numpy.dot,
(mo_coeff.T, Imat, mp._scf.get_ovlp(), mo_coeff)) * -1
dm1mo = numpy.zeros((nmo, nmo))
if with_frozen:
dco = Imat[OF[:, None], OA] / (mo_energy[OF, None] - mo_energy[OA])
dfv = Imat[VF[:, None], VA] / (mo_energy[VF, None] - mo_energy[VA])
dm1mo[OA[:, None], OA] = doo + doo.T
dm1mo[OF[:, None], OA] = dco
dm1mo[OA[:, None], OF] = dco.T
dm1mo[VA[:, None], VA] = dvv + dvv.T
dm1mo[VF[:, None], VA] = dfv
dm1mo[VA[:, None], VF] = dfv.T
else:
dm1mo[:nocc, :nocc] = doo + doo.T
dm1mo[nocc:, nocc:] = dvv + dvv.T
dm1 = reduce(numpy.dot, (mo_coeff, dm1mo, mo_coeff.T))
vhf = mp._scf.get_veff(mp.mol, dm1) * 2
Xvo = reduce(numpy.dot, (mo_coeff[:, nocc:].T, vhf, mo_coeff[:, :nocc]))
Xvo += Imat[:nocc, nocc:].T - Imat[nocc:, :nocc]
dm1mo += _response_dm1(mp, Xvo)
time1 = log.timer_debug1('response_rdm1 intermediates', *time1)
Imat[nocc:, :nocc] = Imat[:nocc, nocc:].T
im1 = reduce(numpy.dot, (mo_coeff, Imat, mo_coeff.T))
time1 = log.timer_debug1('response_rdm1', *time1)
log.debug('h1 and JK1')
# Initialize hcore_deriv with the underlying SCF object because some
# extensions (e.g. QM/MM, solvent) modifies the SCF object only.
mf_grad = mp_grad.base._scf.nuc_grad_method()
hcore_deriv = mf_grad.hcore_generator(mol)
s1 = mf_grad.get_ovlp(mol)
zeta = lib.direct_sum('i+j->ij', mo_energy, mo_energy) * .5
zeta[nocc:, :nocc] = mo_energy[:nocc]
zeta[:nocc, nocc:] = mo_energy[:nocc].reshape(-1, 1)
zeta = reduce(numpy.dot, (mo_coeff, zeta * dm1mo, mo_coeff.T))
dm1 = reduce(numpy.dot, (mo_coeff, dm1mo, mo_coeff.T))
p1 = numpy.dot(mo_coeff[:, :nocc], mo_coeff[:, :nocc].T)
vhf_s1occ = reduce(numpy.dot, (p1, mp._scf.get_veff(mol, dm1 + dm1.T), p1))
time1 = log.timer_debug1('h1 and JK1', *time1)
# Hartree-Fock part contribution
dm1p = hf_dm1 + dm1 * 2
dm1 += hf_dm1
zeta += rhf_grad.make_rdm1e(mo_energy, mo_coeff, mp.mo_occ)
for k, ia in enumerate(atmlst):
shl0, shl1, p0, p1 = offsetdic[ia]
# s[1] dot I, note matrix im1 is not hermitian
de[k] += numpy.einsum('xij,ij->x', s1[:, p0:p1], im1[p0:p1])
de[k] += numpy.einsum('xji,ij->x', s1[:, p0:p1], im1[:, p0:p1])
# h[1] \dot DM, contribute to f1
h1ao = hcore_deriv(ia)
de[k] += numpy.einsum('xij,ji->x', h1ao, dm1)
# -s[1]*e \dot DM, contribute to f1
de[k] -= numpy.einsum('xij,ij->x', s1[:, p0:p1], zeta[p0:p1])
de[k] -= numpy.einsum('xji,ij->x', s1[:, p0:p1], zeta[:, p0:p1])
# -vhf[s_ij[1]], contribute to f1, *2 for s1+s1.T
de[k] -= numpy.einsum('xij,ij->x', s1[:, p0:p1], vhf_s1occ[p0:p1]) * 2
de[k] -= numpy.einsum('xij,ij->x', vhf1[k], dm1p)
log.timer('%s gradients' % mp.__class__.__name__, *time0)
return de
def update_amps(cc, t1, t2, eris, max_memory=2000):
time0 = time.clock(), time.time()
log = logger.Logger(cc.stdout, cc.verbose)
nocc, nvir = t1.shape
fock = eris.fock
fov = fock[:nocc, nocc:]
foo = fock[:nocc, :nocc]
fvv = fock[nocc:, nocc:]
mo_e = eris.fock.diagonal()
eia = mo_e[:nocc, None] - mo_e[None, nocc:]
eijab = lib.direct_sum('ia,jb->ijab', eia, eia)
Foo = imd.cc_Foo(t1, t2, eris)
Fvv = imd.cc_Fvv(t1, t2, eris)
Fov = imd.cc_Fov(t1, t2, eris)
Loo = imd.Loo(t1, t2, eris)
Lvv = imd.Lvv(t1, t2, eris)
Woooo = imd.cc_Woooo(t1, t2, eris)
Wvvvv = imd.cc_Wvvvv(t1, t2, eris)
Wvoov = imd.cc_Wvoov(t1, t2, eris)
Wvovo = imd.cc_Wvovo(t1, t2, eris)
# Move energy terms to the other side
Foo -= foo
Fvv -= fvv
Loo -= foo
Lvv -= fvv
# T1 equation
# TODO: Check this conj(). Hirata and Bartlett has
# f_{vo}(a,i), which should be equal to f_{ov}^*(i,a)
t1new = fov.conj().copy()
t1new += -2 * einsum('kc,ka,ic->ia', fov, t1, t1)
t1new += einsum('ac,ic->ia', Fvv, t1)
t1new += -einsum('ki,ka->ia', Foo, t1)
t1new += einsum('kc,kica->ia', Fov, 2 * t2)
t1new += einsum('kc,ikca->ia', Fov, -t2)
t1new += einsum('kc,ic,ka->ia', Fov, t1, t1)
t1new += 2 * einsum('akic,kc->ia', eris.voov, t1)
t1new += -einsum('kaic,kc->ia', eris.ovov, t1)
t1new += 2 * einsum('akcd,ikcd->ia', eris.vovv, t2)
t1new += -einsum('akdc,ikcd->ia', eris.vovv, t2)
t1new += 2 * einsum('akcd,ic,kd->ia', eris.vovv, t1, t1)
t1new += -einsum('akdc,ic,kd->ia', eris.vovv, t1, t1)
t1new += -2 * einsum('klic,klac->ia', eris.ooov, t2)
t1new += einsum('lkic,klac->ia', eris.ooov, t2)
t1new += -2 * einsum('klic,ka,lc->ia', eris.ooov, t1, t1)
t1new += einsum('lkic,ka,lc->ia', eris.ooov, t1, t1)
# T2 equation
# For conj(), see Hirata and Bartlett, Eq. (36)
t2new = np.array(eris.oovv).conj()
t2new += einsum('klij,klab->ijab', Woooo, t2)
t2new += einsum('klij,ka,lb->ijab', Woooo, t1, t1)
for a in range(nvir):
Wvvvv_a = np.array(Wvvvv[a])
t2new[:, :, a, :] += einsum('bcd,ijcd->ijb', Wvvvv_a, t2)
t2new[:, :, a, :] += einsum('bcd,ic,jd->ijb', Wvvvv_a, t1, t1)
tmp = einsum('ac,ijcb->ijab', Lvv, t2)
t2new += (tmp + tmp.transpose(1, 0, 3, 2))
tmp = einsum('ki,kjab->ijab', Loo, t2)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
tmp2 = np.array(eris.vovv).transpose(3,2,1,0).conj() \
- einsum('kbic,ka->abic',eris.ovov,t1)
tmp = einsum('abic,jc->ijab', tmp2, t1)
t2new += (tmp + tmp.transpose(1, 0, 3, 2))
tmp2 = np.array(eris.ooov).transpose(3,2,1,0).conj() \
+ einsum('akic,jc->akij',eris.voov,t1)
tmp = einsum('akij,kb->ijab', tmp2, t1)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
tmp = 2 * einsum('akic,kjcb->ijab', Wvoov, t2) - einsum(
'akci,kjcb->ijab', Wvovo, t2)
t2new += (tmp + tmp.transpose(1, 0, 3, 2))
tmp = einsum('akic,kjbc->ijab', Wvoov, t2)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
tmp = einsum('bkci,kjac->ijab', Wvovo, t2)
t2new -= (tmp + tmp.transpose(1, 0, 3, 2))
t1new /= eia
t2new /= eijab
time0 = log.timer_debug1('update t1 t2', *time0)
return t1new, t2new
def solve_mo1(sscobj, h1):
cput1 = (time.clock(), time.time())
log = logger.Logger(sscobj.stdout, sscobj.verbose)
mol = sscobj.mol
mo_energy = sscobj._scf.mo_energy
mo_coeff = sscobj._scf.mo_coeff
mo_occ = sscobj._scf.mo_occ
h1aa, h1ab, h1ba, h1bb = h1
nset = len(h1aa)
eai_aa = 1. / lib.direct_sum('a-i->ai', mo_energy[0][mo_occ[0] == 0],
mo_energy[0][mo_occ[0] > 0])
eai_ab = 1. / lib.direct_sum('a-i->ai', mo_energy[0][mo_occ[0] == 0],
mo_energy[1][mo_occ[1] > 0])
eai_ba = 1. / lib.direct_sum('a-i->ai', mo_energy[1][mo_occ[1] == 0],
mo_energy[0][mo_occ[0] > 0])
eai_bb = 1. / lib.direct_sum('a-i->ai', mo_energy[1][mo_occ[1] == 0],
mo_energy[1][mo_occ[1] > 0])
mo1 = (numpy.asarray(h1aa) * -eai_aa, numpy.asarray(h1ab) * -eai_ab,
numpy.asarray(h1ba) * -eai_ba, numpy.asarray(h1bb) * -eai_bb)
h1aa = h1ab = h1ba = h1bb = None
if not sscobj.cphf:
return mo1
orboa = mo_coeff[0][:, mo_occ[0] > 0]
orbva = mo_coeff[0][:, mo_occ[0] == 0]
orbob = mo_coeff[1][:, mo_occ[1] > 0]
orbvb = mo_coeff[1][:, mo_occ[1] == 0]
nocca = orboa.shape[1]
nvira = orbva.shape[1]
noccb = orbob.shape[1]
nvirb = orbvb.shape[1]
p1 = nvira * nocca
p2 = p1 + nvira * noccb
p3 = p2 + nvirb * nocca
def _split_mo1(mo1):
mo1 = mo1.reshape(nset, -1)
mo1aa = mo1[:, :p1].reshape(nset, nvira, nocca)
mo1ab = mo1[:, p1:p2].reshape(nset, nvira, noccb)
mo1ba = mo1[:, p2:p3].reshape(nset, nvirb, nocca)
mo1bb = mo1[:, p3:].reshape(nset, nvirb, noccb)
return mo1aa, mo1ab, mo1ba, mo1bb
mo1 = numpy.hstack((mo1[0].reshape(nset, -1), mo1[1].reshape(nset, -1),
mo1[2].reshape(nset, -1), mo1[3].reshape(nset, -1)))
vresp = _gen_uhf_response(mf, with_j=False, hermi=0)
mo_va_oa = numpy.asarray(numpy.hstack((orbva, orboa)), order='F')
mo_va_ob = numpy.asarray(numpy.hstack((orbva, orbob)), order='F')
mo_vb_oa = numpy.asarray(numpy.hstack((orbvb, orboa)), order='F')
mo_vb_ob = numpy.asarray(numpy.hstack((orbvb, orbob)), order='F')
def vind(mo1):
mo1aa, mo1ab, mo1ba, mo1bb = _split_mo1(mo1)
dm1aa = _dm1_mo2ao(mo1aa, orbva, orboa)
dm1ab = _dm1_mo2ao(mo1ab, orbva, orbob)
dm1ba = _dm1_mo2ao(mo1ba, orbvb, orboa)
dm1bb = _dm1_mo2ao(mo1bb, orbvb, orbob)
# imaginary Hermitian
dm1 = numpy.vstack([
dm1aa - dm1aa.transpose(0, 2, 1), dm1ab - dm1ba.transpose(0, 2, 1),
dm1ba - dm1ab.transpose(0, 2, 1), dm1bb - dm1bb.transpose(0, 2, 1)
])
v1 = vresp(dm1)
v1aa = _ao2mo.nr_e2(v1[:nset], mo_va_oa,
(0, nvira, nvira, nvira + nocca))
v1ab = _ao2mo.nr_e2(v1[nset * 1:nset * 2], mo_va_ob,
(0, nvira, nvira, nvira + noccb))
v1ba = _ao2mo.nr_e2(v1[nset * 2:nset * 3], mo_vb_oa,
(0, nvirb, nvirb, nvirb + nocca))
v1bb = _ao2mo.nr_e2(v1[nset * 3:], mo_vb_ob,
(0, nvirb, nvirb, nvirb + noccb))
v1aa = v1aa.reshape(nset, nvira, nocca)
v1ab = v1ab.reshape(nset, nvira, noccb)
v1ba = v1ba.reshape(nset, nvirb, nocca)
v1bb = v1bb.reshape(nset, nvirb, noccb)
v1aa *= eai_aa
v1ab *= eai_ab
v1ba *= eai_ba
v1bb *= eai_bb
v1mo = numpy.hstack((v1aa.reshape(nset, -1), v1ab.reshape(nset, -1),
v1ba.reshape(nset, -1), v1bb.reshape(nset, -1)))
return v1mo.ravel()
mo1 = lib.krylov(vind, mo1.ravel(), tol=1e-9, max_cycle=20, verbose=log)
log.timer('solving FC CPHF eqn', *cput1)
mo1 = _split_mo1(mo1)
return mo1
def kernel(mycc,
t1=None,
t2=None,
l1=None,
l2=None,
eris=None,
atmlst=None,
mf_grad=None,
verbose=logger.INFO):
if t1 is None: t1 = mycc.t1
if t2 is None: t2 = mycc.t2
if l1 is None: l1 = mycc.l1
if l2 is None: l2 = mycc.l2
if eris is None: eris = ccsd._ERIS(mycc)
if mf_grad is None:
mf_grad = rhf_grad.Gradients(mycc._scf)
log = logger.Logger(mycc.stdout, mycc.verbose)
time0 = time.clock(), time.time()
mol = mycc.mol
if mycc.frozen is not 0:
raise NotImplementedError('frozen orbital ccsd_grad')
moidx = ccsd.get_moidx(mycc)
mo_coeff = mycc.mo_coeff[:,
moidx] #FIXME: ensure mycc.mo_coeff is canonical orbital
mo_energy = eris.fock.diagonal()
nocc, nvir = t1.shape
nao, nmo = mo_coeff.shape
nao_pair = nao * (nao + 1) // 2
log.debug('Build ccsd rdm1 intermediates')
d1 = ccsd_rdm.gamma1_intermediates(mycc, t1, t2, l1, l2)
doo, dov, dvo, dvv = d1
time1 = log.timer('rdm1 intermediates', *time0)
log.debug('Build ccsd rdm2 intermediates')
d2 = ccsd_rdm.gamma2_incore(mycc, t1, t2, l1, l2)
time1 = log.timer('rdm2 intermediates', *time1)
log.debug('Build ccsd response_rdm1')
Ioo, Ivv, Ivo, Xvo = IX_intermediates(mycc, t1, t2, l1, l2, eris, d1, d2)
time1 = log.timer('response_rdm1 intermediates', *time1)
dm1mo = response_dm1(mycc, t1, t2, l1, l2, eris, (Ioo, Ivv, Ivo, Xvo))
dm1mo[:nocc, :nocc] = doo * 2
dm1mo[nocc:, nocc:] = dvv * 2
dm1ao = reduce(numpy.dot, (mo_coeff, dm1mo, mo_coeff.T))
im1 = numpy.zeros_like(dm1mo)
im1[:nocc, :nocc] = Ioo
im1[nocc:, nocc:] = Ivv
im1[nocc:, :nocc] = Ivo
im1[:nocc, nocc:] = Ivo.T
im1 = reduce(numpy.dot, (mo_coeff, im1, mo_coeff.T))
time1 = log.timer('response_rdm1', *time1)
log.debug('symmetrized rdm2 and MO->AO transformation')
dm1_with_hf = dm1mo.copy()
for i in range(nocc):
dm1_with_hf[i, i] += 1
dm2ao = _rdm2_mo2ao(mycc, d2, dm1_with_hf, mo_coeff)
time1 = log.timer('MO->AO transformation', *time1)
log.debug('h1 and JK1')
h1 = mf_grad.get_hcore(mol)
s1 = mf_grad.get_ovlp(mol)
zeta = lib.direct_sum('i+j->ij', mo_energy, mo_energy) * .5
zeta[nocc:, :nocc] = mo_energy[:nocc]
zeta[:nocc, nocc:] = mo_energy[:nocc].reshape(-1, 1)
zeta = reduce(numpy.dot, (mo_coeff, zeta * dm1mo, mo_coeff.T))
p1 = numpy.dot(mo_coeff[:, :nocc], mo_coeff[:, :nocc].T)
vhf4sij = reduce(numpy.dot,
(p1, mycc._scf.get_veff(mol, dm1ao + dm1ao.T), p1))
time1 = log.timer('h1 and JK1', *time1)
# Hartree-Fock part contribution
hf_dm1 = mycc._scf.make_rdm1(mycc.mo_coeff, mycc.mo_occ)
dm1ao += hf_dm1
zeta += mf_grad.make_rdm1e(mycc.mo_energy, mycc.mo_coeff, mycc.mo_occ)
if atmlst is None:
atmlst = range(mol.natm)
offsetdic = mol.offset_nr_by_atom()
de = numpy.zeros((len(atmlst), 3))
for k, ia in enumerate(atmlst):
shl0, shl1, p0, p1 = offsetdic[ia]
# s[1] dot I, note matrix im1 is not hermitian
de[k] = (numpy.einsum('xij,ij->x', s1[:, p0:p1], im1[p0:p1]) +
numpy.einsum('xji,ij->x', s1[:, p0:p1], im1[:, p0:p1]))
# h[1] \dot DM, *2 for +c.c., contribute to f1
h1ao = mf_grad._grad_rinv(mol, ia)
h1ao[:, p0:p1] += h1[:, p0:p1]
de[k] += (numpy.einsum('xij,ij->x', h1ao, dm1ao) +
numpy.einsum('xji,ij->x', h1ao, dm1ao))
# -s[1]*e \dot DM, contribute to f1
de[k] -= (numpy.einsum('xij,ij->x', s1[:, p0:p1], zeta[p0:p1]) +
numpy.einsum('xji,ij->x', s1[:, p0:p1], zeta[:, p0:p1]))
# -vhf[s_ij[1]], contribute to f1, *2 for s1+s1.T
de[k] -= numpy.einsum('xij,ij->x', s1[:, p0:p1], vhf4sij[p0:p1]) * 2
# 2e AO integrals dot 2pdm
eri1 = mol.intor('int2e_ip1',
comp=3,
aosym='s2kl',
shls_slice=(shl0, shl1, 0, mol.nbas, 0, mol.nbas, 0,
mol.nbas))
eri1 = eri1.reshape(3, p1 - p0, nao, -1)
dm2buf = _load_block_tril(dm2ao, p0, p1)
de[k] -= numpy.einsum('xijk,ijk->x', eri1, dm2buf) * 2
eri1 = dm2buf = None
log.debug('grad of atom %d %s = %s', ia, mol.atom_symbol(ia), de[k])
time1 = log.timer('grad of atom %d' % ia, *time1)
de += rhf_grad.grad_nuc(mol)
log.note('CCSD gradinets')
log.note('==============')
log.note(' x y z')
for k, ia in enumerate(atmlst):
log.note('%d %s %15.9f %15.9f %15.9f', ia, mol.atom_symbol(ia),
*de[k])
log.timer('CCSD gradients', *time0)
return de
def mol_to_xyg3_grad(mol):
print("In mol_to_xyg3_grad", flush=True)
nmo = mol.nao
nocc = mol.nelec[0]
nvir = nmo - nocc
so = slice(0, nocc)
sv = slice(nocc, nmo)
sa = slice(0, nmo)
scfh = GGAHelper(mol, "b3lypg", mol_to_grids(mol))
nch = GGAHelper(mol, "0.8033*HF - 0.0140*LDA + 0.2107*B88, 0.6789*LYP", mol_to_grids(mol), init_scf=False)
ncgga = NCGGAEngine(scfh, nch)
e, eo, ev = scfh.e, scfh.eo, scfh.ev
C, Co, Cv = scfh.C, scfh.Co, scfh.Cv
eri0_mo = scfh.eri0_mo
eri1_ao = scfh.eri1_ao
S_1_mo = scfh.S_1_mo
F_1_mo = scfh.F_1_mo
Ax0_Core = scfh.Ax0_Core
D_iajb = lib.direct_sum("i - a + j - b", scfh.eo, scfh.ev, scfh.eo, scfh.ev)
t_iajb = eri0_mo[so, sv, so, sv] / D_iajb
T_iajb = 2 * t_iajb - t_iajb.swapaxes(1, 3)
D_r = np.zeros((nmo, nmo))
D_r[so, so] += - 2 * np.einsum("iakb, jakb -> ij", T_iajb, t_iajb)
D_r[sv, sv] += 2 * np.einsum("iajc, ibjc -> ab", T_iajb, t_iajb)
L = np.zeros((nvir, nocc))
L += Ax0_Core(sv, so, sa, sa)(D_r)
L -= 4 * np.einsum("jakb, ijbk -> ai", T_iajb, eri0_mo[so, so, sv, so])
L += 4 * np.einsum("ibjc, abjc -> ai", T_iajb, eri0_mo[sv, sv, so, sv])
D_r[sv, so] = scf.cphf.solve(Ax0_Core(sv, so, sv, so), e, scfh.mo_occ, L, max_cycle=100, tol=1e-13)[0]
# W[I] - Correct with s1-im1 term in PySCF
D_WI = np.zeros((nmo, nmo))
D_WI[so, so] = - 2 * np.einsum("iakb, jakb -> ij", T_iajb, eri0_mo[so, sv, so, sv])
D_WI[sv, sv] = - 2 * np.einsum("iajc, ibjc -> ab", T_iajb, eri0_mo[so, sv, so, sv])
D_WI[sv, so] = - 4 * np.einsum("jakb, ijbk -> ai", T_iajb, eri0_mo[so, so, sv, so])
# W[II] - Correct with s1-zeta term in PySCF
# Note that zeta in PySCF includes HF energy weighted density rdm1e
# The need of scaler 1 in D_WII[sv, so] is that Aikens use doubled P
D_WII = np.zeros((nmo, nmo))
D_WII[so, so] = - 0.5 * D_r[so, so] * lib.direct_sum("i + j -> ij", eo, eo)
D_WII[sv, sv] = - 0.5 * D_r[sv, sv] * lib.direct_sum("a + b -> ab", ev, ev)
D_WII[sv, so] = - D_r[sv, so] * eo
# W[III] - Correct with s1-vhf_s1occ term in PySCF
D_WIII = np.zeros((nmo, nmo))
D_WIII[so, so] = - 0.5 * Ax0_Core(so, so, sa, sa)(D_r)
# Summation
D_W = D_WI + D_WII + D_WIII
# Non-seperatable - Correct with `de` generated in PySCF code part --2e AO integrals dot 2pdm--
D_pdm2_NS = 2 * np.einsum("iajb, ui, va, kj, lb -> uvkl", T_iajb, Co, Cv, Co, Cv)
grad_B3LYP_MP2 = (
+ (D_r * F_1_mo).sum(axis=(-1, -2))
+ (D_W * S_1_mo).sum(axis=(-1, -2))
+ (D_pdm2_NS * eri1_ao).sum(axis=(-1, -2, -3, -4))
)
return ncgga.E_1 + 0.3211 * grad_B3LYP_MP2
def kernel(tdgrad,
z,
atmlst=None,
mf_grad=None,
max_memory=2000,
verbose=logger.INFO):
mol = tdgrad.mol
mf = tdgrad.base._scf
mo_coeff = mf.mo_coeff
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
nao, nmo = mo_coeff.shape
nocc = (mo_occ > 0).sum()
nvir = nmo - nocc
#eai = lib.direct_sum('a-i->ai', mo_energy[nocc:], mo_energy[:nocc])
z = z[0].reshape(nocc, nvir).T
orbv = mo_coeff[:, nocc:]
orbo = mo_coeff[:, :nocc]
def fvind(x):
dm = numpy.einsum('pi,xij,qj->xpq', orbv, x, orbo)
v_ao = mf.get_veff(mol, (dm + dm.transpose(0, 2, 1))) * 2
return numpy.einsum('pi,xpq,qj->xij', orbv, v_ao, orbo).reshape(3, -1)
h1 = rhf_grad.get_hcore(mol)
s1 = rhf_grad.get_ovlp(mol)
eri1 = -mol.intor('int2e_ip1', aosym='s1', comp=3)
eri1 = eri1.reshape(3, nao, nao, nao, nao)
eri0 = ao2mo.kernel(mol, mo_coeff)
eri0 = ao2mo.restore(1, eri0, nmo).reshape(nmo, nmo, nmo, nmo)
g = eri0 * 2 - eri0.transpose(0, 3, 2, 1)
zeta = lib.direct_sum('i+j->ij', mo_energy, mo_energy) * .5
zeta[nocc:, :nocc] = mo_energy[:nocc]
zeta[:nocc, nocc:] = mo_energy[nocc:]
if atmlst is None:
atmlst = range(mol.natm)
offsetdic = mol.offset_nr_by_atom()
de = numpy.zeros((len(atmlst), 3))
for k, ia in enumerate(atmlst):
shl0, shl1, p0, p1 = offsetdic[ia]
mol.set_rinv_origin(mol.atom_coord(ia))
h1ao = -mol.atom_charge(ia) * mol.intor('int1e_iprinv', comp=3)
h1ao[:, p0:p1] += h1[:, p0:p1]
h1ao = h1ao + h1ao.transpose(0, 2, 1)
h1mo = numpy.einsum('pi,xpq,qj->xij', mo_coeff, h1ao, mo_coeff)
s1mo = numpy.einsum('pi,xpq,qj->xij', mo_coeff[p0:p1], s1[:, p0:p1],
mo_coeff)
s1mo = s1mo + s1mo.transpose(0, 2, 1)
f1 = h1mo - numpy.einsum('xpq,pq->xpq', s1mo, zeta)
f1 -= numpy.einsum('klpq,xlk->xpq', g[:nocc, :nocc],
s1mo[:, :nocc, :nocc])
eri1a = eri1.copy()
eri1a[:, :p0] = 0
eri1a[:, p1:] = 0
eri1a = eri1a + eri1a.transpose(0, 2, 1, 3, 4)
eri1a = eri1a + eri1a.transpose(0, 3, 4, 1, 2)
g1 = numpy.einsum('xpjkl,pi->xijkl', eri1a, mo_coeff)
g1 = numpy.einsum('xipkl,pj->xijkl', g1, mo_coeff)
g1 = numpy.einsum('xijpl,pk->xijkl', g1, mo_coeff)
g1 = numpy.einsum('xijkp,pl->xijkl', g1, mo_coeff)
g1 = g1 * 2 - g1.transpose(0, 1, 4, 3, 2)
f1 += numpy.einsum('xkkpq->xpq', g1[:, :nocc, :nocc])
f1ai = f1[:, nocc:, :nocc].copy()
c1 = s1mo * -.5
c1vo = cphf.solve(fvind, mo_energy, mo_occ, f1ai, max_cycle=50)[0]
c1[:, nocc:, :nocc] = c1vo
c1[:, :nocc,
nocc:] = -(s1mo[:, nocc:, :nocc] + c1vo).transpose(0, 2, 1)
f1 += numpy.einsum('kapq,xak->xpq', g[:nocc, nocc:], c1vo)
f1 += numpy.einsum('akpq,xak->xpq', g[nocc:, :nocc], c1vo)
e1 = numpy.einsum('xaijb,ai,bj->x', g1[:, nocc:, :nocc, :nocc, nocc:],
z, z)
e1 += numpy.einsum('xab,ai,bi->x', f1[:, nocc:, nocc:], z, z)
e1 -= numpy.einsum('xij,ai,aj->x', f1[:, :nocc, :nocc], z, z)
g1 = numpy.einsum('pjkl,xpi->xijkl', g, c1)
g1 += numpy.einsum('ipkl,xpj->xijkl', g, c1)
g1 += numpy.einsum('ijpl,xpk->xijkl', g, c1)
g1 += numpy.einsum('ijkp,xpl->xijkl', g, c1)
e1 += numpy.einsum('xaijb,ai,bj->x', g1[:, nocc:, :nocc, :nocc, nocc:],
z, z)
de[k] = e1
return de
def update_lambda(mycc, t1, t2, l1, l2, eris, imds):
"""
Update GCCSD lambda.
"""
time0 = logger.process_clock(), logger.perf_counter()
log = logger.Logger(mycc.stdout, mycc.verbose)
t1T = t1.T
t2T = np.asarray(t2.transpose(2, 3, 0, 1), order='C')
t1 = t2 = None
nvir_seg, nvir, nocc = t2T.shape[:3]
l1T = l1.T
l2T = np.asarray(l2.transpose(2, 3, 0, 1), order='C')
l1 = l2 = None
ntasks = mpi.pool.size
vlocs = [_task_location(nvir, task_id) for task_id in range(ntasks)]
vloc0, vloc1 = vlocs[rank]
log.debug2('vlocs %s', vlocs)
assert vloc1 - vloc0 == nvir_seg
fvo = eris.fock[nocc:, :nocc]
mo_e_o = eris.mo_energy[:nocc]
mo_e_v = eris.mo_energy[nocc:] + mycc.level_shift
v1 = imds.v1 - np.diag(mo_e_v)
v2 = imds.v2 - np.diag(mo_e_o)
mba = einsum('cakl, cbkl -> ba', l2T, t2T) * 0.5
mba = mpi.allreduce_inplace(mba)
mij = einsum('cdki, cdkj -> ij', l2T, t2T) * 0.5
mij = mpi.allreduce_inplace(mij)
# m3 [a]bij
m3 = einsum('abkl, ijkl -> abij', l2T, np.asarray(imds.woooo))
tauT = t2T #+ np.einsum('ai, bj -> abij', t1T[vloc0:vloc1] * 2.0, t1T, optimize=True)
tmp = einsum('cdij, cdkl -> ijkl', l2T, tauT)
tmp = mpi.allreduce_inplace(tmp)
tauT = None
vvoo = np.asarray(eris.xvoo)
tmp = einsum('abkl, ijkl -> abij', vvoo, tmp)
tmp *= 0.25
m3 += tmp
tmp = None
#tmp = einsum('cdij, dk -> ckij', l2T, t1T)
#for task_id, tmp, p0, p1 in _rotate_vir_block(tmp, vlocs=vlocs):
# m3 -= einsum('kcba, ckij -> abij', eris.ovvx[:, p0:p1], tmp)
# tmp = None
eris_vvvv = eris.xvvv.transpose(2, 3, 0, 1)
tmp_2 = np.empty_like(l2T) # used for line 387
for task_id, l2T_tmp, p0, p1 in _rotate_vir_block(l2T, vlocs=vlocs):
tmp = einsum('cdij, cdab -> abij', l2T_tmp, eris_vvvv[p0:p1])
tmp *= 0.5
m3 += tmp
tmp_2[:, p0:p1] = einsum('acij, cb -> baij', l2T_tmp, v1[:,
vloc0:vloc1])
tmp = l2T_tmp = None
eris_vvvv = None
#l1Tnew = einsum('abij, bj -> ai', m3, t1T)
#l1Tnew = mpi.allgather(l1Tnew)
l1Tnew = np.zeros_like(l1T)
l2Tnew = m3
l2Tnew += vvoo
#fvo1 = fvo #+ mpi.allreduce(einsum('cbkj, ck -> bj', vvoo, t1T[vloc0:vloc1]))
#tmp = np.einsum('ai, bj -> abij', l1T[vloc0:vloc1], fvo1, optimize=True)
tmp = 0.0
wvovo = np.asarray(imds.wovvo).transpose(1, 0, 2, 3)
for task_id, w_tmp, p0, p1 in _rotate_vir_block(wvovo, vlocs=vlocs):
tmp -= einsum('acki, cjbk -> abij', l2T[:, p0:p1], w_tmp)
w_tmp = None
wvovo = None
tmp = tmp - tmp.transpose(0, 1, 3, 2)
l2Tnew += tmp
tmpT = mpi.alltoall_new([tmp[:, p0:p1] for p0, p1 in vlocs],
split_recvbuf=True)
for task_id, (p0, p1) in enumerate(vlocs):
tmp = tmpT[task_id].reshape(p1 - p0, nvir_seg, nocc, nocc)
l2Tnew[:, p0:p1] -= tmp.transpose(1, 0, 2, 3)
tmp = None
#tmp = einsum('ak, ijkb -> baij', l1T, eris.ooox)
#tmp -= tmp_2
tmp = -tmp_2
tmp1vv = mba #+ np.dot(t1T, l1T.T) # ba
tmp -= einsum('ca, bcij -> baij', tmp1vv, vvoo)
l2Tnew += tmp
tmpT = mpi.alltoall_new([tmp[:, p0:p1] for p0, p1 in vlocs],
split_recvbuf=True)
for task_id, (p0, p1) in enumerate(vlocs):
tmp = tmpT[task_id].reshape(p1 - p0, nvir_seg, nocc, nocc)
l2Tnew[:, p0:p1] -= tmp.transpose(1, 0, 2, 3)
tmp = None
#tmp = einsum('jcab, ci -> baji', eris.ovvx, -l1T)
tmp = einsum('abki, jk -> abij', l2T, v2)
tmp1oo = mij #+ np.dot(l1T.T, t1T) # ik
tmp -= einsum('ik, abkj -> abij', tmp1oo, vvoo)
vvoo = None
l2Tnew += tmp
l2Tnew -= tmp.transpose(0, 1, 3, 2)
tmp = None
#l1Tnew += fvo
#tmp = einsum('bj, ibja -> ai', -l1T[vloc0:vloc1], eris.oxov)
#l1Tnew += np.dot(v1.T, l1T)
#l1Tnew -= np.dot(l1T, v2.T)
#tmp -= einsum('cakj, icjk -> ai', l2T, imds.wovoo)
#tmp -= einsum('bcak, bcik -> ai', imds.wvvvo, l2T)
#tmp += einsum('baji, bj -> ai', l2T, imds.w3[vloc0:vloc1])
#tmp_2 = t1T[vloc0:vloc1] - np.dot(tmp1vv[vloc0:vloc1], t1T)
#tmp_2 -= np.dot(t1T[vloc0:vloc1], mij)
#tmp_2 += einsum('bcjk, ck -> bj', t2T, l1T)
#tmp += einsum('baji, bj -> ai', vvoo, tmp_2)
#tmp_2 = None
#tmp += einsum('icab, bc -> ai', eris.oxvv, tmp1vv[:, vloc0:vloc1])
#l1Tnew += mpi.allreduce(tmp)
#l1Tnew -= mpi.allgather(einsum('jika, kj -> ai', eris.ooox, tmp1oo))
#tmp = fvo - mpi.allreduce(einsum('bakj, bj -> ak', vvoo, t1T[vloc0:vloc1]))
#vvoo = None
#l1Tnew -= np.dot(tmp, mij.T)
#l1Tnew -= np.dot(mba.T, tmp)
eia = mo_e_o[:, None] - mo_e_v
#l1Tnew /= eia.T
for i in range(vloc0, vloc1):
l2Tnew[i - vloc0] /= lib.direct_sum('i + jb -> bij', eia[:, i], eia)
time0 = log.timer_debug1('update l1 l2', *time0)
return l1Tnew.T, l2Tnew.transpose(2, 3, 0, 1)
def _gamma2_intermediates(mycc,
t1,
t2,
l1,
l2,
eris=None,
compress_vvvv=False):
d2 = uccsd_rdm._gamma2_intermediates(mycc, t1, t2, l1, l2)
if eris is None: eris = mycc.ao2mo()
dovov, dovOV, dOVov, dOVOV = d2[0]
dvvvv, dvvVV, dVVvv, dVVVV = d2[1]
doooo, dooOO, dOOoo, dOOOO = d2[2]
doovv, dooVV, dOOvv, dOOVV = d2[3]
dovvo, dovVO, dOVvo, dOVVO = d2[4]
dvvov, dvvOV, dVVov, dVVOV = d2[5]
dovvv, dovVV, dOVvv, dOVVV = d2[6]
dooov, dooOV, dOOov, dOOOV = d2[7]
t1a, t1b = t1
t2aa, t2ab, t2bb = t2
nocca, noccb, nvira, nvirb = t2ab.shape
nmoa = eris.focka.shape[0]
nmob = eris.fockb.shape[0]
mo_ea = eris.focka.diagonal().real
mo_eb = eris.fockb.diagonal().real
eia = mo_ea[:nocca, None] - mo_ea[nocca:]
eIA = mo_eb[:noccb, None] - mo_eb[noccb:]
fvo = eris.focka[nocca:, :nocca]
fVO = eris.fockb[noccb:, :noccb]
# aaa
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eia, eia, eia)
w = numpy.einsum('ijae,kceb->ijkabc', t2aa,
numpy.asarray(eris.get_ovvv()).conj())
w -= numpy.einsum('mkbc,iajm->ijkabc', t2aa,
numpy.asarray(eris.ovoo.conj()))
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.ovov).conj(), t1a)
v += numpy.einsum('jkbc,ai->ijkabc', t2aa, fvo) * .5
rw = r6(p6(w)) / d3
wvd = r6(p6(w * 2 + v)) / d3
dovov += numpy.einsum('ia,ijkabc->jbkc', t1a, rw.conj()) * 0.25
# *(1/8) instead of (1/4) because ooov appears 4 times in the 2pdm tensor due
# to symmetrization, and its contribution is scaled by 1/2 in Tr(H,2pdm)
dooov -= numpy.einsum('mkbc,ijkabc->jmia', t2aa, wvd.conj()) * .125
dovvv += numpy.einsum('kjcf,ijkabc->iafb', t2aa, wvd.conj()) * .125
# bbb
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eIA, eIA, eIA)
w = numpy.einsum('ijae,kceb->ijkabc', t2bb,
numpy.asarray(eris.get_OVVV()).conj())
w -= numpy.einsum('imab,kcjm->ijkabc', t2bb,
numpy.asarray(eris.OVOO.conj()))
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.OVOV).conj(), t1b)
v += numpy.einsum('jkbc,ai->ijkabc', t2bb, fVO) * .5
rw = r6(p6(w)) / d3
wvd = r6(p6(w * 2 + v)) / d3
dOVOV += numpy.einsum('ia,ijkabc->jbkc', t1b, rw.conj()) * .25
dOOOV -= numpy.einsum('mkbc,ijkabc->jmia', t2bb, wvd.conj()) * .125
dOVVV += numpy.einsum('kjcf,ijkabc->iafb', t2bb, wvd.conj()) * .125
# baa
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eIA, eia, eia)
w = numpy.einsum('jIeA,kceb->IjkAbc', t2ab,
numpy.asarray(eris.get_ovvv()).conj()) * 2
w += numpy.einsum('jIbE,kcEA->IjkAbc', t2ab,
numpy.asarray(eris.get_ovVV()).conj()) * 2
w += numpy.einsum('jkbe,IAec->IjkAbc', t2aa,
numpy.asarray(eris.get_OVvv()).conj())
w -= numpy.einsum('mIbA,kcjm->IjkAbc', t2ab,
numpy.asarray(eris.ovoo).conj()) * 2
w -= numpy.einsum('jMbA,kcIM->IjkAbc', t2ab,
numpy.asarray(eris.ovOO).conj()) * 2
w -= numpy.einsum('jmbc,IAkm->IjkAbc', t2aa,
numpy.asarray(eris.OVoo).conj())
v = numpy.einsum('jbkc,IA->IjkAbc', numpy.asarray(eris.ovov).conj(), t1b)
v += numpy.einsum('kcIA,jb->IjkAbc', numpy.asarray(eris.ovOV).conj(), t1a)
v += numpy.einsum('kcIA,jb->IjkAbc', numpy.asarray(eris.ovOV).conj(), t1a)
v += numpy.einsum('jkbc,AI->IjkAbc', t2aa, fVO) * .5
v += numpy.einsum('kIcA,bj->IjkAbc', t2ab, fvo) * 2
rw = r4(w) / d3
wvd = r4(w * 2 + v) / d3
dovvv += numpy.einsum('jiea,ijkabc->kceb', t2ab, wvd.conj()) * .25
dovVV += numpy.einsum('jibe,ijkabc->kcea', t2ab, wvd.conj()) * .25
dOVvv += numpy.einsum('jkbe,ijkabc->iaec', t2aa, wvd.conj()) * .125
dooov -= numpy.einsum('miba,ijkabc->jmkc', t2ab, wvd.conj()) * .25
dOOov -= numpy.einsum('jmba,ijkabc->imkc', t2ab, wvd.conj()) * .25
dooOV -= numpy.einsum('jmbc,ijkabc->kmia', t2aa, wvd.conj()) * .125
dovov += numpy.einsum('ia,ijkabc->jbkc', t1b, rw.conj()) * .25
#dOVov += numpy.einsum('jb,ijkabc->iakc', t1a, rw.conj()) * .25
dovOV += numpy.einsum('jb,ijkabc->kcia', t1a, rw.conj()) * .25
# bba
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eia, eIA, eIA)
w = numpy.einsum('ijae,kceb->ijkabc', t2ab,
numpy.asarray(eris.get_OVVV()).conj()) * 2
w += numpy.einsum('ijeb,kcea->ijkabc', t2ab,
numpy.asarray(eris.get_OVvv()).conj()) * 2
w += numpy.einsum('jkbe,iaec->ijkabc', t2bb,
numpy.asarray(eris.get_ovVV()).conj())
w -= numpy.einsum('imab,kcjm->ijkabc', t2ab,
numpy.asarray(eris.OVOO).conj()) * 2
w -= numpy.einsum('mjab,kcim->ijkabc', t2ab,
numpy.asarray(eris.OVoo).conj()) * 2
w -= numpy.einsum('jmbc,iakm->ijkabc', t2bb,
numpy.asarray(eris.ovOO).conj())
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.OVOV).conj(), t1a)
v += numpy.einsum('iakc,jb->ijkabc', numpy.asarray(eris.ovOV).conj(), t1b)
v += numpy.einsum('iakc,jb->ijkabc', numpy.asarray(eris.ovOV).conj(), t1b)
v += numpy.einsum('JKBC,ai->iJKaBC', t2bb, fvo) * .5
v += numpy.einsum('iKaC,BJ->iJKaBC', t2ab, fVO) * 2
rw = r4(w) / d3
wvd = r4(w * 2 + v) / d3
dOVVV += numpy.einsum('ijae,ijkabc->kceb', t2ab, wvd.conj()) * .25
dOVvv += numpy.einsum('ijeb,ijkabc->kcea', t2ab, wvd.conj()) * .25
dovVV += numpy.einsum('jkbe,ijkabc->iaec', t2bb, wvd.conj()) * .125
dOOOV -= numpy.einsum('imab,ijkabc->jmkc', t2ab, wvd.conj()) * .25
dooOV -= numpy.einsum('mjab,ijkabc->imkc', t2ab, wvd.conj()) * .25
dOOov -= numpy.einsum('jmbc,ijkabc->kmia', t2bb, wvd.conj()) * .125
dOVOV += numpy.einsum('ia,ijkabc->jbkc', t1a, rw.conj()) * .25
dovOV += numpy.einsum('jb,ijkabc->iakc', t1b, rw.conj()) * .25
#dOVov += numpy.einsum('jb,ijkabc->kcia', t1b, rw.conj()) * .25
if compress_vvvv:
nmoa, nmob = mycc.nmo
nocca, noccb, nvira, nvirb = t2ab.shape
idxa = numpy.tril_indices(nvira)
idxa = idxa[0] * nvira + idxa[1]
idxb = numpy.tril_indices(nvirb)
idxb = idxb[0] * nvirb + idxb[1]
dvvvv = dvvvv + dvvvv.transpose(1, 0, 2, 3)
dvvvv = lib.take_2d(dvvvv.reshape(nvira**2, nvira**2), idxa, idxa)
dvvvv *= .5
dvvVV = dvvVV + dvvVV.transpose(1, 0, 2, 3)
dvvVV = lib.take_2d(dvvVV.reshape(nvira**2, nvirb**2), idxa, idxb)
dVVVV = dVVVV + dVVVV.transpose(1, 0, 2, 3)
dVVVV = lib.take_2d(dVVVV.reshape(nvirb**2, nvirb**2), idxb, idxb)
dVVVV *= .5
d2 = ((dovov, dovOV, dOVov, dOVOV), (dvvvv, dvvVV, dVVvv, dVVVV),
(doooo, dooOO, dOOoo, dOOOO), (doovv, dooVV, dOOvv, dOOVV),
(dovvo, dovVO, dOVvo, dOVVO), (dvvov, dvvOV, dVVov, dVVOV),
(dovvv, dovVV, dOVvv, dOVVV), (dooov, dooOV, dOOov, dOOOV))
return d2
def kernel(td_grad,
x_y,
singlet=True,
atmlst=None,
max_memory=2000,
verbose=logger.INFO):
log = logger.new_logger(td_grad, verbose)
time0 = time.clock(), time.time()
mol = td_grad.mol
mf = td_grad.base._scf
mo_coeff = mf.mo_coeff
mo_energy = mf.mo_energy
mo_occ = mf.mo_occ
nao, nmo = mo_coeff.shape
nocc = (mo_occ > 0).sum()
nvir = nmo - nocc
x, y = x_y
xpy = (x + y).reshape(nocc, nvir).T
xmy = (x - y).reshape(nocc, nvir).T
orbv = mo_coeff[:, nocc:]
orbo = mo_coeff[:, :nocc]
dvv = numpy.einsum('ai,bi->ab', xpy, xpy) + numpy.einsum(
'ai,bi->ab', xmy, xmy)
doo = -numpy.einsum('ai,aj->ij', xpy, xpy) - numpy.einsum(
'ai,aj->ij', xmy, xmy)
dmzvop = reduce(numpy.dot, (orbv, xpy, orbo.T))
dmzvom = reduce(numpy.dot, (orbv, xmy, orbo.T))
dmzoo = reduce(numpy.dot, (orbo, doo, orbo.T))
dmzoo += reduce(numpy.dot, (orbv, dvv, orbv.T))
mem_now = lib.current_memory()[0]
max_memory = max(2000, td_grad.max_memory * .9 - mem_now)
ni = mf._numint
ni.libxc.test_deriv_order(mf.xc, 3, raise_error=True)
omega, alpha, hyb = ni.rsh_and_hybrid_coeff(mf.xc, mol.spin)
# dm0 = mf.make_rdm1(mo_coeff, mo_occ), but it is not used when computing
# fxc since rho0 is passed to fxc function.
dm0 = None
rho0, vxc, fxc = ni.cache_xc_kernel(mf.mol,
mf.grids,
mf.xc, [mo_coeff] * 2,
[mo_occ * .5] * 2,
spin=1)
f1vo, f1oo, vxc1, k1ao = \
_contract_xc_kernel(td_grad, mf.xc, dmzvop,
dmzoo, True, True, singlet, max_memory)
if abs(hyb) > 1e-10:
dm = (dmzoo, dmzvop + dmzvop.T, dmzvom - dmzvom.T)
vj, vk = mf.get_jk(mol, dm, hermi=0)
vk *= hyb
if abs(omega) > 1e-10:
vk += rks._get_k_lr(mol, dm, omega) * (alpha - hyb)
veff0doo = vj[0] * 2 - vk[0] + f1oo[0] + k1ao[0] * 2
wvo = reduce(numpy.dot, (orbv.T, veff0doo, orbo)) * 2
if singlet:
veff = vj[1] * 2 - vk[1] + f1vo[0] * 2
else:
veff = -vk[1] + f1vo[0] * 2
veff0mop = reduce(numpy.dot, (mo_coeff.T, veff, mo_coeff))
wvo -= numpy.einsum('ki,ai->ak', veff0mop[:nocc, :nocc], xpy) * 2
wvo += numpy.einsum('ac,ai->ci', veff0mop[nocc:, nocc:], xpy) * 2
veff = -vk[2]
veff0mom = reduce(numpy.dot, (mo_coeff.T, veff, mo_coeff))
wvo -= numpy.einsum('ki,ai->ak', veff0mom[:nocc, :nocc], xmy) * 2
wvo += numpy.einsum('ac,ai->ci', veff0mom[nocc:, nocc:], xmy) * 2
else:
vj = mf.get_j(mol, (dmzoo, dmzvop + dmzvop.T), hermi=1)
veff0doo = vj[0] * 2 + f1oo[0] + k1ao[0] * 2
wvo = reduce(numpy.dot, (orbv.T, veff0doo, orbo)) * 2
if singlet:
veff = vj[1] * 2 + f1vo[0] * 2
else:
veff = f1vo[0] * 2
veff0mop = reduce(numpy.dot, (mo_coeff.T, veff, mo_coeff))
wvo -= numpy.einsum('ki,ai->ak', veff0mop[:nocc, :nocc], xpy) * 2
wvo += numpy.einsum('ac,ai->ci', veff0mop[nocc:, nocc:], xpy) * 2
veff0mom = numpy.zeros((nmo, nmo))
def fvind(x):
# Cannot make call to .base.get_vind because first order orbitals are solved
# through closed shell ground state CPHF.
dm = reduce(numpy.dot, (orbv, x.reshape(nvir, nocc), orbo.T))
dm = dm + dm.T
# Call singlet XC kernel contraction, for closed shell ground state
vindxc = numint.nr_rks_fxc_st(ni, mol, mf.grids, mf.xc, dm0, dm, 0,
singlet, rho0, vxc, fxc, max_memory)
if abs(hyb) > 1e-10:
vj, vk = mf.get_jk(mol, dm)
veff = vj * 2 - hyb * vk + vindxc
if abs(omega) > 1e-10:
veff -= rks._get_k_lr(mol, dm, omega, hermi=1) * (alpha - hyb)
else:
vj = mf.get_j(mol, dm)
veff = vj * 2 + vindxc
return reduce(numpy.dot, (orbv.T, veff, orbo)).ravel()
z1 = cphf.solve(fvind,
mo_energy,
mo_occ,
wvo,
max_cycle=td_grad.cphf_max_cycle,
tol=td_grad.cphf_conv_tol)[0]
z1 = z1.reshape(nvir, nocc)
time1 = log.timer('Z-vector using CPHF solver', *time0)
z1ao = reduce(numpy.dot, (orbv, z1, orbo.T))
# Note Z-vector is always associated to singlet integrals.
fxcz1 = _contract_xc_kernel(td_grad, mf.xc, z1ao, None, False, False, True,
max_memory)[0]
if abs(hyb) > 1e-10:
vj, vk = mf.get_jk(mol, z1ao, hermi=0)
veff = vj * 2 - hyb * vk + fxcz1[0]
if abs(omega) > 1e-10:
veff -= rks._get_k_lr(mol, z1ao, omega) * (alpha - hyb)
else:
vj = mf.get_j(mol, z1ao, hermi=1)
veff = vj * 2 + fxcz1[0]
im0 = numpy.zeros((nmo, nmo))
im0[:nocc, :nocc] = reduce(numpy.dot, (orbo.T, veff0doo + veff, orbo))
im0[:nocc, :nocc] += numpy.einsum('ak,ai->ki', veff0mop[nocc:, :nocc], xpy)
im0[:nocc, :nocc] += numpy.einsum('ak,ai->ki', veff0mom[nocc:, :nocc], xmy)
im0[nocc:, nocc:] = numpy.einsum('ci,ai->ac', veff0mop[nocc:, :nocc], xpy)
im0[nocc:, nocc:] += numpy.einsum('ci,ai->ac', veff0mom[nocc:, :nocc], xmy)
im0[nocc:, :nocc] = numpy.einsum('ki,ai->ak', veff0mop[:nocc, :nocc],
xpy) * 2
im0[nocc:, :nocc] += numpy.einsum('ki,ai->ak', veff0mom[:nocc, :nocc],
xmy) * 2
zeta = lib.direct_sum('i+j->ij', mo_energy, mo_energy) * .5
zeta[nocc:, :nocc] = mo_energy[:nocc]
zeta[:nocc, nocc:] = mo_energy[nocc:]
dm1 = numpy.zeros((nmo, nmo))
dm1[:nocc, :nocc] = doo
dm1[nocc:, nocc:] = dvv
dm1[nocc:, :nocc] = z1
dm1[:nocc, :nocc] += numpy.eye(nocc) * 2 # for ground state
im0 = reduce(numpy.dot, (mo_coeff, im0 + zeta * dm1, mo_coeff.T))
hcore_deriv = td_grad.hcore_generator(mol)
s1 = td_grad.get_ovlp(mol)
dmz1doo = z1ao + dmzoo
oo0 = reduce(numpy.dot, (orbo, orbo.T))
if abs(hyb) > 1e-10:
dm = (oo0, dmz1doo + dmz1doo.T, dmzvop + dmzvop.T, dmzvom - dmzvom.T)
vj, vk = td_grad.get_jk(mol, dm)
vk *= hyb
if abs(omega) > 1e-10:
with mol.with_range_coulomb(omega):
vk += td_grad.get_k(mol, dm) * (alpha - hyb)
vj = vj.reshape(-1, 3, nao, nao)
vk = vk.reshape(-1, 3, nao, nao)
if singlet:
veff1 = vj * 2 - vk
else:
veff1 = numpy.vstack((vj[:2] * 2 - vk[:2], -vk[2:]))
else:
vj = td_grad.get_j(mol, (oo0, dmz1doo + dmz1doo.T, dmzvop + dmzvop.T))
vj = vj.reshape(-1, 3, nao, nao)
veff1 = numpy.zeros((4, 3, nao, nao))
if singlet:
veff1[:3] = vj * 2
else:
veff1[:2] = vj[:2] * 2
veff1[0] += vxc1[1:]
veff1[1] += (f1oo[1:] + fxcz1[1:] +
k1ao[1:] * 2) * 2 # *2 for dmz1doo+dmz1oo.T
veff1[2] += f1vo[1:] * 2
time1 = log.timer('2e AO integral derivatives', *time1)
if atmlst is None:
atmlst = range(mol.natm)
offsetdic = mol.offset_nr_by_atom()
de = numpy.zeros((len(atmlst), 3))
for k, ia in enumerate(atmlst):
shl0, shl1, p0, p1 = offsetdic[ia]
# Ground state gradients
h1ao = hcore_deriv(ia)
h1ao[:, p0:p1] += veff1[0, :, p0:p1]
h1ao[:, :, p0:p1] += veff1[0, :, p0:p1].transpose(0, 2, 1)
# oo0*2 for doubly occupied orbitals
e1 = numpy.einsum('xpq,pq->x', h1ao, oo0) * 2
e1 += numpy.einsum('xpq,pq->x', h1ao, dmz1doo)
e1 -= numpy.einsum('xpq,pq->x', s1[:, p0:p1], im0[p0:p1])
e1 -= numpy.einsum('xqp,pq->x', s1[:, p0:p1], im0[:, p0:p1])
e1 += numpy.einsum('xij,ij->x', veff1[1, :, p0:p1], oo0[p0:p1])
e1 += numpy.einsum('xij,ij->x', veff1[2, :, p0:p1],
dmzvop[p0:p1, :]) * 2
e1 += numpy.einsum('xij,ij->x', veff1[3, :, p0:p1],
dmzvom[p0:p1, :]) * 2
e1 += numpy.einsum('xji,ij->x', veff1[2, :, p0:p1], dmzvop[:,
p0:p1]) * 2
e1 -= numpy.einsum('xji,ij->x', veff1[3, :, p0:p1], dmzvom[:,
p0:p1]) * 2
de[k] = e1
log.timer('TDDFT nuclear gradients', *time0)
return de
def _gamma1_intermediates(mycc, t1, t2, l1, l2, eris=None, for_grad=False):
d1 = uccsd_rdm._gamma1_intermediates(mycc, t1, t2, l1, l2)
if eris is None: eris = mycc.ao2mo()
t1a, t1b = t1
t2aa, t2ab, t2bb = t2
nocca, noccb, nvira, nvirb = t2ab.shape
nmoa = eris.focka.shape[0]
nmob = eris.fockb.shape[0]
mo_ea = eris.focka.diagonal().real
mo_eb = eris.fockb.diagonal().real
eia = mo_ea[:nocca, None] - mo_ea[nocca:]
eIA = mo_eb[:noccb, None] - mo_eb[noccb:]
fvo = eris.focka[nocca:, :nocca]
fVO = eris.fockb[noccb:, :noccb]
# aaa
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eia, eia, eia)
w = numpy.einsum('ijae,kceb->ijkabc', t2aa,
numpy.asarray(eris.get_ovvv()).conj())
w -= numpy.einsum('mkbc,iajm->ijkabc', t2aa,
numpy.asarray(eris.ovoo.conj()))
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.ovov).conj(), t1a)
v += numpy.einsum('jkbc,ai->ijkabc', t2aa, fvo) * .5
rw = p6(r6(w)) / d3
wvd = p6(w + v) / d3
goo = numpy.einsum('iklabc,jklabc->ij', wvd.conj(), rw) * .125
gvv = numpy.einsum('ijkacd,ijkbcd->ab', wvd, rw.conj()) * .125
gvo = numpy.einsum('jkbc,ijkabc->ai', t2aa.conj(), rw) * .125
# bbb
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eIA, eIA, eIA)
w = numpy.einsum('ijae,kceb->ijkabc', t2bb,
numpy.asarray(eris.get_OVVV()).conj())
w -= numpy.einsum('imab,kcjm->ijkabc', t2bb,
numpy.asarray(eris.OVOO.conj()))
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.OVOV).conj(), t1b)
v += numpy.einsum('jkbc,ai->ijkabc', t2bb, fVO) * .5
rw = p6(r6(w)) / d3
wvd = p6(w + v) / d3
gOO = numpy.einsum('iklabc,jklabc->ij', wvd.conj(), rw) * .125
gVV = numpy.einsum('ijkacd,ijkbcd->ab', wvd, rw.conj()) * .125
gVO = numpy.einsum('jkbc,ijkabc->ai', t2bb.conj(), rw) * .125
# baa
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eIA, eia, eia)
w = numpy.einsum('jIeA,kceb->IjkAbc', t2ab,
numpy.asarray(eris.get_ovvv()).conj()) * 2
w += numpy.einsum('jIbE,kcEA->IjkAbc', t2ab,
numpy.asarray(eris.get_ovVV()).conj()) * 2
w += numpy.einsum('jkbe,IAec->IjkAbc', t2aa,
numpy.asarray(eris.get_OVvv()).conj())
w -= numpy.einsum('mIbA,kcjm->IjkAbc', t2ab,
numpy.asarray(eris.ovoo).conj()) * 2
w -= numpy.einsum('jMbA,kcIM->IjkAbc', t2ab,
numpy.asarray(eris.ovOO).conj()) * 2
w -= numpy.einsum('jmbc,IAkm->IjkAbc', t2aa,
numpy.asarray(eris.OVoo).conj())
v = numpy.einsum('jbkc,IA->IjkAbc', numpy.asarray(eris.ovov).conj(), t1b)
v += numpy.einsum('kcIA,jb->IjkAbc', numpy.asarray(eris.ovOV).conj(), t1a)
v += numpy.einsum('kcIA,jb->IjkAbc', numpy.asarray(eris.ovOV).conj(), t1a)
v += numpy.einsum('jkbc,AI->IjkAbc', t2aa, fVO) * .5
v += numpy.einsum('kIcA,bj->IjkAbc', t2ab, fvo) * 2
rw = r4(w) / d3
wvd = (w + v) / d3
goo += numpy.einsum('kilabc,kjlabc->ij', wvd.conj(), rw) * .25
goo += numpy.einsum('kliabc,kljabc->ij', wvd.conj(), rw) * .25
gOO += numpy.einsum('iklabc,jklabc->ij', wvd.conj(), rw) * .25
gvv += numpy.einsum('ijkcad,ijkcbd->ab', wvd, rw.conj()) * .25
gvv += numpy.einsum('ijkcda,ijkcdb->ab', wvd, rw.conj()) * .25
gVV += numpy.einsum('ijkacd,ijkbcd->ab', wvd, rw.conj()) * .25
gvo += numpy.einsum('kica,ijkabc->bj', t2ab.conj(), rw) * .5
gVO += numpy.einsum('jkbc,ijkabc->ai', t2aa.conj(), rw) * .125
# bba
d3 = lib.direct_sum('ia+jb+kc->ijkabc', eia, eIA, eIA)
w = numpy.einsum('ijae,kceb->ijkabc', t2ab,
numpy.asarray(eris.get_OVVV()).conj()) * 2
w += numpy.einsum('ijeb,kcea->ijkabc', t2ab,
numpy.asarray(eris.get_OVvv()).conj()) * 2
w += numpy.einsum('jkbe,iaec->ijkabc', t2bb,
numpy.asarray(eris.get_ovVV()).conj())
w -= numpy.einsum('imab,kcjm->ijkabc', t2ab,
numpy.asarray(eris.OVOO).conj()) * 2
w -= numpy.einsum('mjab,kcim->ijkabc', t2ab,
numpy.asarray(eris.OVoo).conj()) * 2
w -= numpy.einsum('jmbc,iakm->ijkabc', t2bb,
numpy.asarray(eris.ovOO).conj())
v = numpy.einsum('jbkc,ia->ijkabc', numpy.asarray(eris.OVOV).conj(), t1a)
v += numpy.einsum('iakc,jb->ijkabc', numpy.asarray(eris.ovOV).conj(), t1b)
v += numpy.einsum('iakc,jb->ijkabc', numpy.asarray(eris.ovOV).conj(), t1b)
v += numpy.einsum('JKBC,ai->iJKaBC', t2bb, fvo) * .5
v += numpy.einsum('iKaC,BJ->iJKaBC', t2ab, fVO) * 2
rw = r4(w) / d3
wvd = (w + v) / d3
goo += numpy.einsum('iklabc,jklabc->ij', wvd.conj(), rw) * .25
gOO += numpy.einsum('kilabc,kjlabc->ij', wvd.conj(), rw) * .25
gOO += numpy.einsum('kliabc,kljabc->ij', wvd.conj(), rw) * .25
gvv += numpy.einsum('ijkacd,ijkbcd->ab', wvd, rw.conj()) * .25
gVV += numpy.einsum('ijkcad,ijkcbd->ab', wvd, rw.conj()) * .25
gVV += numpy.einsum('ijkcda,ijkcdb->ab', wvd, rw.conj()) * .25
gVO += numpy.einsum('ikac,ijkabc->bj', t2ab.conj(), rw) * .5
gvo += numpy.einsum('jkbc,ijkabc->ai', t2bb.conj(), rw) * .125
doo, dOO = d1[0]
dov, dOV = d1[1]
dvo, dVO = d1[2]
dvv, dVV = d1[3]
if for_grad:
doo -= goo
dOO -= gOO
dvv += gvv
dVV += gVV
else:
doo[numpy.diag_indices(nocca)] -= goo.diagonal()
dOO[numpy.diag_indices(noccb)] -= gOO.diagonal()
dvv[numpy.diag_indices(nvira)] += gvv.diagonal()
dVV[numpy.diag_indices(nvirb)] += gVV.diagonal()
dvo += gvo
dVO += gVO
return d1
def ucphf_with_freq(mf,
mo_energy,
mo_occ,
h1,
freq=0,
max_cycle=20,
tol=1e-9,
hermi=False,
verbose=logger.WARN):
log = logger.new_logger(verbose=verbose)
t0 = (time.clock(), time.time())
occidxa = mo_occ[0] > 0
occidxb = mo_occ[1] > 0
viridxa = ~occidxa
viridxb = ~occidxb
mo_ea, mo_eb = mo_energy
# e_ai - freq may produce very small elements which can cause numerical
# issue in krylov solver
LEVEL_SHIF = 0.1
e_ai_a = lib.direct_sum('a-i->ai', mo_ea[viridxa], mo_ea[occidxa]).ravel()
e_ai_b = lib.direct_sum('a-i->ai', mo_eb[viridxb], mo_eb[occidxb]).ravel()
diag = (e_ai_a - freq, e_ai_b - freq, e_ai_a + freq, e_ai_b + freq)
diag[0][diag[0] < LEVEL_SHIF] += LEVEL_SHIF
diag[1][diag[1] < LEVEL_SHIF] += LEVEL_SHIF
diag[2][diag[2] < LEVEL_SHIF] += LEVEL_SHIF
diag[3][diag[3] < LEVEL_SHIF] += LEVEL_SHIF
mo0a, mo0b = mf.mo_coeff
nao, nmoa = mo0a.shape
nmob = mo0b.shape
orbva = mo0a[:, viridxa]
orbvb = mo0b[:, viridxb]
orboa = mo0a[:, occidxa]
orbob = mo0b[:, occidxb]
nvira = orbva.shape[1]
nvirb = orbvb.shape[1]
nocca = orboa.shape[1]
noccb = orbob.shape[1]
h1a = h1[0].reshape(-1, nvira * nocca)
h1b = h1[1].reshape(-1, nvirb * noccb)
ncomp = h1a.shape[0]
mo1base = numpy.hstack(
(-h1a / diag[0], -h1b / diag[1], -h1a / diag[2], -h1b / diag[3]))
offsets = numpy.cumsum((nocca * nvira, noccb * nvirb, nocca * nvira))
vresp = _gen_uhf_response(mf, hermi=0)
def vind(xys):
nz = len(xys)
dm1a = numpy.empty((nz, nao, nao))
dm1b = numpy.empty((nz, nao, nao))
for i in range(nz):
xa, xb, ya, yb = numpy.split(xys[i], offsets)
dmx = reduce(numpy.dot, (orbva, xa.reshape(nvira, nocca), orboa.T))
dmy = reduce(numpy.dot,
(orboa, ya.reshape(nvira, nocca).T, orbva.T))
dm1a[i] = dmx + dmy # AX + BY
dmx = reduce(numpy.dot, (orbvb, xb.reshape(nvirb, noccb), orbob.T))
dmy = reduce(numpy.dot,
(orbob, yb.reshape(nvirb, noccb).T, orbvb.T))
dm1b[i] = dmx + dmy # AX + BY
v1ao = vresp(numpy.stack((dm1a, dm1b)))
v1voa = lib.einsum('xpq,pi,qj->xij', v1ao[0], orbva,
orboa).reshape(nz, -1)
v1vob = lib.einsum('xpq,pi,qj->xij', v1ao[1], orbvb,
orbob).reshape(nz, -1)
v1ova = lib.einsum('xpq,pi,qj->xji', v1ao[0], orboa,
orbva).reshape(nz, -1)
v1ovb = lib.einsum('xpq,pi,qj->xji', v1ao[1], orbob,
orbvb).reshape(nz, -1)
for i in range(nz):
xa, xb, ya, yb = numpy.split(xys[i], offsets)
v1voa[i] += (e_ai_a - freq - diag[0]) * xa
v1voa[i] /= diag[0]
v1vob[i] += (e_ai_b - freq - diag[1]) * xb
v1vob[i] /= diag[1]
v1ova[i] += (e_ai_a + freq - diag[2]) * ya
v1ova[i] /= diag[2]
v1ovb[i] += (e_ai_b + freq - diag[3]) * yb
v1ovb[i] /= diag[3]
v = numpy.hstack((v1voa, v1vob, v1ova, v1ovb))
return v
# FIXME: krylov solver is not accurate enough for many freqs. Using tight
# tol and lindep could offer small help. A better linear equation solver
# is needed.
mo1 = lib.krylov(vind,
mo1base,
tol=tol,
max_cycle=max_cycle,
hermi=hermi,
lindep=1e-18,
verbose=log)
log.timer('krylov solver in CPHF', *t0)
dm1a = numpy.empty((ncomp, nao, nao))
dm1b = numpy.empty((ncomp, nao, nao))
for i in range(ncomp):
xa, xb, ya, yb = numpy.split(mo1[i], offsets)
dmx = reduce(numpy.dot, (orbva, xa.reshape(nvira, nocca) * 2, orboa.T))
dmy = reduce(numpy.dot,
(orboa, ya.reshape(nvira, nocca).T * 2, orbva.T))
dm1a[i] = dmx + dmy
dmx = reduce(numpy.dot, (orbvb, xb.reshape(nvirb, noccb) * 2, orbob.T))
dmy = reduce(numpy.dot,
(orbob, yb.reshape(nvirb, noccb).T * 2, orbvb.T))
dm1b[i] = dmx + dmy
v1ao = vresp(numpy.stack((dm1a, dm1b)))
mo_e1_a = lib.einsum('xpq,pi,qj->xij', v1ao[0], orboa, orboa)
mo_e1_b = lib.einsum('xpq,pi,qj->xij', v1ao[1], orbob, orbob)
mo_e1 = (mo_e1_a, mo_e1_b)
xa, xb, ya, yb = numpy.split(mo1, offsets, axis=1)
mo1 = (xa.reshape(ncomp, nvira, nocca), xb.reshape(ncomp, nvirb, noccb),
ya.reshape(ncomp, nvira, nocca), yb.reshape(ncomp, nvirb, noccb))
return mo1, mo_e1
def update_amps_independent_compressions(
cc,
t1: np.ndarray,
t2: np.ndarray,
eris: ccsd._ChemistsERIs,
):
"""Update the CC t1 and t2 amplitudes using a compressed t2 tensor for
several of the contractions.
Parameters
----------
cc : fricc.FRILCCSD
CC object
t1 : np.ndarray
t1 amplitudes (nocc,nvirt)
t2 : np.ndarray
t2 amplitudes (nocc,nocc,nvirt,nvirt)
eris : ccsd._ChemistsERIs
2e-integrals
Returns
-------
(np.ndarray,np.ndarray)
The new t1 and t2 amplitudes
Notes
-----
Ref: Taube and Bartlett J. Chem. Phys. 130, 144112 (2009) Eq. 13 and 15
"""
#
# Check Args
#
assert isinstance(eris, ccsd._ChemistsERIs)
log = lib.logger.new_logger(cc)
m_keep = cc.fri_settings["m_keep"]
# TODO add input checks
m_keep = cc.fri_settings["m_keep"]
if m_keep > t2.size or m_keep == 0:
raise ValueError(
"Bad m_keep value! The following condition wasn't met 0 < m_keep <= t2.size"
)
compressed_contractions = cc.fri_settings["compressed_contractions"]
contraction_timings = {}
#
# Shorthands
#
nocc, nvir = t1.shape
fock = eris.fock
mo_e_o = eris.mo_energy[:nocc]
mo_e_v = eris.mo_energy[nocc:] + cc.level_shift
fov = fock[:nocc, nocc:].copy()
t_update_amps = time.perf_counter()
#
# Compression
#
log.debug(f"M_KEEP = {m_keep} of {t2.size}")
# log.warn(f"|t2|_1 = {np.linalg.norm(t2.ravel(), ord=1)}")
# np.save("fricc_t2.npy", t2.ravel())
# exit(0)
t_compress = time.perf_counter()
t2_sparse = [
SparseTensor4d(
t2,
t2.shape,
int(m_keep),
cc.fri_settings["compression"],
cc.fri_settings["sampling_method"],
cc.fri_settings["verbose"],
)
for _ in range(6)
]
t_compress = time.perf_counter() - t_compress
#
# Updating the Amplitudes
#
Foo = fock[:nocc, :nocc].copy()
Fvv = fock[nocc:, nocc:].copy()
Fov = fock[:nocc, nocc:].copy()
# Move energy terms to the other side
Foo[np.diag_indices(nocc)] -= mo_e_o
Fvv[np.diag_indices(nvir)] -= mo_e_v
###############
# T1 equation #
###############
eris_ovoo = np.asarray(eris.ovoo, order="C")
eris_ovvv = np.asarray(eris.get_ovvv())
if cc.fri_settings["LCCD"]:
t1 = np.zeros_like(t1)
t1new = np.zeros_like(t1) # DO LCCD
else:
t1new = np.zeros_like(t1)
# Term 1
t1new += fov.conj()
# Term 2
t1new += np.einsum("ac,ic->ia", Fvv, t1)
# Term 3
t1new += -np.einsum("ki,ka->ia", Foo, t1)
# Term 4
t1new += 2 * np.einsum("kcai,kc->ia", eris.ovvo, t1)
t1new += -np.einsum("kiac,kc->ia", eris.oovv, t1)
# Term 5
t1new += 2 * lib.einsum("kdac,ikcd->ia", eris_ovvv, t2)
t1new += -lib.einsum("kcad,ikcd->ia", eris_ovvv, t2)
# Term 6
t1new += -2 * lib.einsum("lcki,klac->ia", eris_ovoo, t2)
t1new += lib.einsum("kcli,klac->ia", eris_ovoo, t2)
# Term 7
t1new += 2 * np.einsum("kc,kica->ia", Fov, t2)
t1new += -np.einsum("kc,ikca->ia", Fov, t2)
###############
# T2 equation #
###############
# Term 1
t2new = np.zeros_like(t2)
t2new += np.asarray(eris.ovov).conj().transpose(0, 2, 1, 3)
# Term 2
tmp = lib.einsum("ki,kjab->ijab", Foo, t2)
t2new -= tmp + tmp.transpose(1, 0, 3, 2)
# Term 3
tmp = lib.einsum("ac,ijcb->ijab", Fvv, t2)
t2new += tmp + tmp.transpose(1, 0, 3, 2)
Woooo = np.asarray(eris.oooo).copy().transpose(0, 2, 1, 3)
Wvoov = np.asarray(eris.ovvo).copy().transpose(2, 0, 3, 1)
Wvovo = np.asarray(eris.oovv).copy().transpose(2, 0, 3, 1)
Wvvvv = np.asarray(imd._get_vvvv(eris)).transpose(0, 2, 1, 3)
# Term 4
if "O^2V^4" in compressed_contractions:
t_2323 = time.perf_counter()
contract_DTSpT(Wvvvv, t2_sparse[0], t2new, "2323")
contraction_timings["2323"] = time.perf_counter() - t_2323
else:
t2new += lib.einsum("abcd,ijcd->ijab", Wvvvv, t2)
# Term 5
if "O^4V^2" in compressed_contractions:
t_0101 = time.perf_counter()
contract_DTSpT(Woooo, t2_sparse[1], t2new, "0101")
contraction_timings["0101"] = time.perf_counter() - t_0101
else:
t2new += lib.einsum("klij,klab->ijab", Woooo, t2)
# FRI-Compressed contraction
# Term 6
if "O^3V^3" in compressed_contractions:
tmp = np.zeros_like(t2new)
t_1302 = time.perf_counter()
contract_DTSpT(Wvoov, t2_sparse[2], tmp, "1302")
contraction_timings["1302"] = time.perf_counter() - t_1302
t_1202 = time.perf_counter()
contract_DTSpT(Wvovo, t2_sparse[3], tmp, "1202")
contraction_timings["1202"] = time.perf_counter() - t_1202
t2new += tmp + tmp.transpose(1, 0, 3, 2)
tmp = np.zeros_like(t2new)
t_1303 = time.perf_counter()
contract_DTSpT(Wvoov, t2_sparse[4], tmp, "1303")
contraction_timings["1303"] = time.perf_counter() - t_1303
t2new -= tmp + tmp.transpose(1, 0, 3, 2)
tmp = np.zeros_like(t2new)
t_1203 = time.perf_counter()
contract_DTSpT(Wvovo, t2_sparse[5], tmp, "1203")
contraction_timings["1203"] = time.perf_counter() - t_1203
t2new -= tmp + tmp.transpose(1, 0, 3, 2)
else:
tmp = 2 * lib.einsum("akic,kjcb->ijab", Wvoov, t2)
tmp -= lib.einsum("akci,kjcb->ijab", Wvovo, t2)
t2new += tmp + tmp.transpose(1, 0, 3, 2)
tmp = lib.einsum("akic,kjbc->ijab", Wvoov, t2)
t2new -= tmp + tmp.transpose(1, 0, 3, 2)
tmp = lib.einsum("bkci,kjac->ijab", Wvovo, t2)
t2new -= tmp + tmp.transpose(1, 0, 3, 2)
# Term 7
tmp = lib.einsum("akij,kb->ijab", eris_ovoo.transpose(1, 3, 0, 2).conj(), t1)
t2new -= tmp + tmp.transpose(1, 0, 3, 2)
# Term 8
tmp = lib.einsum("iabc,jc->ijab", np.asarray(eris_ovvv).conj(), t1)
t2new += tmp + tmp.transpose(1, 0, 3, 2)
#
#
eia = mo_e_o[:, None] - mo_e_v
eijab = lib.direct_sum("ia,jb->ijab", eia, eia)
t1new /= eia
t2new /= eijab
#
# Timing
#
t_update_amps = time.perf_counter() - t_update_amps
log.debug(f"\nFRI: Compression Time {t_compress:.3f}")
fri_time = copy.copy(t_compress)
for k, v in contraction_timings.items():
log.debug(f"FRI: Contraction {k} Time: {v:.3f} (s)")
fri_time += v
fri_time_frac = (fri_time) / t_update_amps
log.debug(
f"FRI: CCSD Total Time {t_update_amps:.3f} FRI-related fraction = {fri_time_frac:.3f}\n"
)
return t1new, t2new
def build_se_part(gf2,
eri,
gf_occ,
gf_vir,
nmom,
os_factor=1.0,
ss_factor=1.0):
''' Builds the auxiliaries.
'''
cput0 = (time.clock(), time.time())
log = logger.Logger(gf2.stdout, gf2.verbose)
assert type(gf_occ) is agf2.GreensFunction
assert type(gf_vir) is agf2.GreensFunction
nmo = gf2.nmo
nocc = gf_occ.naux
nvir = gf_vir.naux
tol = gf2.weight_tol
if not (gf2.frozen is None or gf2.frozen == 0):
mask = agf2.ragf2.get_frozen_mask(agf2)
nmo -= np.sum(~mask)
ei, ci = gf_occ.energy, gf_occ.coupling
ea, ca = gf_vir.energy, gf_vir.coupling
qxi, qja = agf2.dfragf2._make_qmo_eris_incore(gf2, eri, (ci, ci, ca))
t = np.zeros((2 * nmom + 2, nmo, nmo))
eija = lib.direct_sum('i,j,a->ija', ei, ei, -ea)
naux = qxi.shape[0]
buf = [np.empty((nmo, nocc * nvir)), np.empty((nmo * nocc, nvir))]
for i in mpi_helper.nrange(nocc):
qx = qxi.reshape(naux, nmo, nocc)[:, :, i]
xija = lib.dot(qx.T, qja, c=buf[0])
xjia = lib.dot(qxi.T, qja[:, i * nvir:(i + 1) * nvir], c=buf[1])
xjia = xjia.reshape(nmo, nocc * nvir)
xjia = 2.0 * xija - xjia #TODO: oo/ss factors
eja = eija[i].ravel()
for n in range(2 * nmom + 2):
t[n] = lib.dot(xija, xjia.T, beta=1, c=t[n])
xjia *= eja[None]
mpi_helper.barrier()
mpi_helper.allreduce_safe_inplace(t)
#t = _agf2.dfragf2_slow_fast_build(qxi, qja, ei, ea, 2*nmom+2, os_factor=os_factor, ss_factor=ss_factor)
if not np.all(np.isfinite(t)):
raise ValueError('Overflow from large moments')
m, b = block_lanczos.block_lanczos(t, nmom + 1)
e, v = block_lanczos.build_from_tridiag(m, b)
se = agf2.SelfEnergy(e, v, chempot=gf_occ.chempot)
se.remove_uncoupled(tol=tol)
if not (gf2.frozen is None or gf2.frozen == 0):
coupling = np.zeros((nmo, se.naux))
coupling[mask] = se.coupling
se = agf2.SelfEnergy(se.energy, coupling, chempot=se.chempot)
log.timer('se part', *cput0)
return se
def get_ab(mf, mo_energy=None, mo_coeff=None, mo_occ=None):
r'''A and B matrices for TDDFT response function.
A[i,a,j,b] = \delta_{ab}\delta_{ij}(E_a - E_i) + (ia||bj)
B[i,a,j,b] = (ia||jb)
'''
if mo_energy is None: mo_energy = mf.mo_energy
if mo_coeff is None: mo_coeff = mf.mo_coeff
if mo_occ is None: mo_occ = mf.mo_occ
assert (mo_coeff.dtype == numpy.double)
mol = mf.mol
nao, nmo = mo_coeff.shape
occidx = numpy.where(mo_occ == 2)[0]
viridx = numpy.where(mo_occ == 0)[0]
orbv = mo_coeff[:, viridx]
orbo = mo_coeff[:, occidx]
nvir = orbv.shape[1]
nocc = orbo.shape[1]
mo = numpy.hstack((orbo, orbv))
nmo = nocc + nvir
e_ia = lib.direct_sum('a-i->ia', mo_energy[viridx], mo_energy[occidx])
a = numpy.diag(e_ia.ravel()).reshape(nocc, nvir, nocc, nvir)
b = numpy.zeros_like(a)
def add_hf_(a, b, hyb=1):
eri_mo = ao2mo.general(mol, [orbo, mo, mo, mo], compact=False)
eri_mo = eri_mo.reshape(nocc, nmo, nmo, nmo)
a += numpy.einsum('iabj->iajb', eri_mo[:nocc, nocc:, nocc:, :nocc]) * 2
a -= numpy.einsum('ijba->iajb', eri_mo[:nocc, :nocc, nocc:,
nocc:]) * hyb
b += numpy.einsum('iajb->iajb', eri_mo[:nocc, nocc:, :nocc, nocc:]) * 2
b -= numpy.einsum('jaib->iajb', eri_mo[:nocc, nocc:, :nocc,
nocc:]) * hyb
if isinstance(mf, scf.hf.KohnShamDFT):
ni = mf._numint
ni.libxc.test_deriv_order(mf.xc, 2, raise_error=True)
if getattr(mf, 'nlc', '') != '':
logger.warn(
mf, 'NLC functional found in DFT object. Its second '
'deriviative is not available. Its contribution is '
'not included in the response function.')
omega, alpha, hyb = ni.rsh_and_hybrid_coeff(mf.xc, mol.spin)
add_hf_(a, b, hyb)
xctype = ni._xc_type(mf.xc)
dm0 = mf.make_rdm1(mo_coeff, mo_occ)
make_rho = ni._gen_rho_evaluator(mol, dm0, hermi=1)[0]
mem_now = lib.current_memory()[0]
max_memory = max(2000, mf.max_memory * .8 - mem_now)
if xctype == 'LDA':
ao_deriv = 0
for ao, mask, weight, coords \
in ni.block_loop(mol, mf.grids, nao, ao_deriv, max_memory):
rho = make_rho(0, ao, mask, 'LDA')
fxc = ni.eval_xc(mf.xc, rho, 0, deriv=2)[2]
frr = fxc[0]
rho_o = lib.einsum('rp,pi->ri', ao, orbo)
rho_v = lib.einsum('rp,pi->ri', ao, orbv)
rho_ov = numpy.einsum('ri,ra->ria', rho_o, rho_v)
w_ov = numpy.einsum('ria,r->ria', rho_ov, weight * frr)
iajb = lib.einsum('ria,rjb->iajb', rho_ov, w_ov) * 2
a += iajb
b += iajb
elif xctype == 'GGA':
ao_deriv = 1
for ao, mask, weight, coords \
in ni.block_loop(mol, mf.grids, nao, ao_deriv, max_memory):
rho = make_rho(0, ao, mask, 'GGA')
vxc, fxc = ni.eval_xc(mf.xc, rho, 0, deriv=2)[1:3]
vgamma = vxc[1]
frho, frhogamma, fgg = fxc[:3]
rho_o = lib.einsum('xrp,pi->xri', ao, orbo)
rho_v = lib.einsum('xrp,pi->xri', ao, orbv)
rho_ov = numpy.einsum('xri,ra->xria', rho_o, rho_v[0])
rho_ov[1:4] += numpy.einsum('ri,xra->xria', rho_o[0],
rho_v[1:4])
# sigma1 ~ \nabla(\rho_\alpha+\rho_\beta) dot \nabla(|b><j|) z_{bj}
sigma1 = numpy.einsum('xr,xria->ria', rho[1:4], rho_ov[1:4])
w_ov = numpy.empty_like(rho_ov)
w_ov[0] = numpy.einsum('r,ria->ria', frho, rho_ov[0])
w_ov[0] += numpy.einsum('r,ria->ria', 2 * frhogamma, sigma1)
f_ov = numpy.einsum('r,ria->ria', 4 * fgg, sigma1)
f_ov += numpy.einsum('r,ria->ria', 2 * frhogamma, rho_ov[0])
w_ov[1:] = numpy.einsum('ria,xr->xria', f_ov, rho[1:4])
w_ov[1:] += numpy.einsum('r,xria->xria', 2 * vgamma,
rho_ov[1:4])
w_ov *= weight[:, None, None]
iajb = lib.einsum('xria,xrjb->iajb', rho_ov, w_ov) * 2
a += iajb
b += iajb
elif xctype == 'NLC':
raise NotImplementedError('NLC')
elif xctype == 'MGGA':
raise NotImplementedError('meta-GGA')
else:
add_hf_(a, b)
return a, b
def make_diagonal(myci, eris):
nocca, noccb = eris.nocc
nmoa = eris.focka.shape[0]
nmob = eris.fockb.shape[1]
nvira = nmoa - nocca
nvirb = nmob - noccb
jdiag_aa = numpy.zeros((nmoa,nmoa))
jdiag_ab = numpy.zeros((nmoa,nmob))
jdiag_bb = numpy.zeros((nmob,nmob))
jdiag_aa[:nocca,:nocca] = numpy.einsum('iijj->ij', eris.oooo)
jdiag_aa[:nocca,nocca:] = numpy.einsum('iijj->ij', eris.oovv)
jdiag_aa[nocca:,:nocca] = jdiag_aa[:nocca,nocca:].T
jdiag_ab[:nocca,:noccb] = numpy.einsum('iijj->ij', eris.ooOO)
jdiag_ab[:nocca,noccb:] = numpy.einsum('iijj->ij', eris.ooVV)
jdiag_ab[nocca:,:noccb] = numpy.einsum('iijj->ji', eris.OOvv)
jdiag_bb[:noccb,:noccb] = numpy.einsum('iijj->ij', eris.OOOO)
jdiag_bb[:noccb,noccb:] = numpy.einsum('iijj->ij', eris.OOVV)
jdiag_bb[noccb:,:noccb] = jdiag_bb[:noccb,noccb:].T
kdiag_aa = numpy.zeros((nmoa,nmoa))
kdiag_bb = numpy.zeros((nmob,nmob))
kdiag_aa[:nocca,:nocca] = numpy.einsum('ijji->ij', eris.oooo)
kdiag_aa[:nocca,nocca:] = numpy.einsum('ijji->ij', eris.ovvo)
kdiag_aa[nocca:,:nocca] = kdiag_aa[:nocca,nocca:].T
kdiag_bb[:noccb,:noccb] = numpy.einsum('ijji->ij', eris.OOOO)
kdiag_bb[:noccb,noccb:] = numpy.einsum('ijji->ij', eris.OVVO)
kdiag_bb[noccb:,:noccb] = kdiag_bb[:noccb,noccb:].T
# if eris.vvvv is not None and eris.vvVV is not None and eris.VVVV is not None:
# def diag_idx(n):
# idx = numpy.arange(n)
# return idx * (idx + 1) // 2 + idx
# jdiag_aa[nocca:,nocca:] = eris.vvvv[diag_idx(nvira)[:,None],diag_idx(nvira)]
# jdiag_ab[nocca:,noccb:] = eris.vvVV[diag_idx(nvira)[:,None],diag_idx(nvirb)]
# jdiag_bb[noccb:,noccb:] = eris.VVVV[diag_idx(nvirb)[:,None],diag_idx(nvirb)]
# kdiag_aa[nocca:,nocca:] = lib.unpack_tril(eris.vvvv.diagonal())
# kdiag_bb[noccb:,noccb:] = lib.unpack_tril(eris.VVVV.diagonal())
jkdiag_aa = jdiag_aa - kdiag_aa
jkdiag_bb = jdiag_bb - kdiag_bb
mo_ea = eris.focka.diagonal()
mo_eb = eris.fockb.diagonal()
ehf = (mo_ea[:nocca].sum() + mo_eb[:noccb].sum()
- jkdiag_aa[:nocca,:nocca].sum() * .5
- jdiag_ab[:nocca,:noccb].sum()
- jkdiag_bb[:noccb,:noccb].sum() * .5)
dia_a = lib.direct_sum('a-i->ia', mo_ea[nocca:], mo_ea[:nocca])
dia_a -= jkdiag_aa[:nocca,nocca:]
dia_b = lib.direct_sum('a-i->ia', mo_eb[noccb:], mo_eb[:noccb])
dia_b -= jkdiag_bb[:noccb,noccb:]
e1diag_a = dia_a + ehf
e1diag_b = dia_b + ehf
e2diag_aa = lib.direct_sum('ia+jb->ijab', dia_a, dia_a)
e2diag_aa += ehf
e2diag_aa += jkdiag_aa[:nocca,:nocca].reshape(nocca,nocca,1,1)
e2diag_aa -= jkdiag_aa[:nocca,nocca:].reshape(nocca,1,1,nvira)
e2diag_aa -= jkdiag_aa[:nocca,nocca:].reshape(1,nocca,nvira,1)
e2diag_aa += jkdiag_aa[nocca:,nocca:].reshape(1,1,nvira,nvira)
e2diag_ab = lib.direct_sum('ia+jb->ijab', dia_a, dia_b)
e2diag_ab += ehf
e2diag_ab += jdiag_ab[:nocca,:noccb].reshape(nocca,noccb,1,1)
e2diag_ab += jdiag_ab[nocca:,noccb:].reshape(1,1,nvira,nvirb)
e2diag_ab -= jdiag_ab[:nocca,noccb:].reshape(nocca,1,1,nvirb)
e2diag_ab -= jdiag_ab[nocca:,:noccb].T.reshape(1,noccb,nvira,1)
e2diag_bb = lib.direct_sum('ia+jb->ijab', dia_b, dia_b)
e2diag_bb += ehf
e2diag_bb += jkdiag_bb[:noccb,:noccb].reshape(noccb,noccb,1,1)
e2diag_bb -= jkdiag_bb[:noccb,noccb:].reshape(noccb,1,1,nvirb)
e2diag_bb -= jkdiag_bb[:noccb,noccb:].reshape(1,noccb,nvirb,1)
e2diag_bb += jkdiag_bb[noccb:,noccb:].reshape(1,1,nvirb,nvirb)
return amplitudes_to_cisdvec(ehf, (e1diag_a, e1diag_b),
(e2diag_aa, e2diag_ab, e2diag_bb))
def make_rdm2(mp, t2=None, eris=None, verbose=logger.NOTE):
r'''
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)
'''
if t2 is None: t2 = mp.t2
nmo = nmo0 = mp.nmo
nocc = nocc0 = mp.nocc
nvir = nmo - nocc
if t2 is None:
if eris is None: eris = mp.ao2mo()
mo_energy = _mo_energy_without_core(mp, mp.mo_energy)
eia = mo_energy[:nocc, None] - mo_energy[None, nocc:]
if not (mp.frozen is 0 or mp.frozen is None):
nmo0 = mp.mo_occ.size
nocc0 = numpy.count_nonzero(mp.mo_occ > 0)
moidx = get_frozen_mask(mp)
oidx = numpy.where(moidx & (mp.mo_occ > 0))[0]
vidx = numpy.where(moidx & (mp.mo_occ == 0))[0]
else:
moidx = oidx = vidx = None
dm1 = make_rdm1(mp, t2, eris, verbose)
dm1[numpy.diag_indices(nocc0)] -= 2
dm2 = numpy.zeros((nmo0, nmo0, nmo0, nmo0),
dtype=dm1.dtype) # Chemist notation
#dm2[:nocc,nocc:,:nocc,nocc:] = t2.transpose(0,3,1,2)*2 - t2.transpose(0,2,1,3)
#dm2[nocc:,:nocc,nocc:,:nocc] = t2.transpose(3,0,2,1)*2 - t2.transpose(2,0,3,1)
for i in range(nocc):
if t2 is None:
gi = numpy.asarray(eris.ovov[i * nvir:(i + 1) * nvir])
gi = gi.reshape(nvir, nocc, nvir).transpose(1, 0, 2)
t2i = gi.conj() / lib.direct_sum('jb+a->jba', eia, eia[i])
else:
t2i = t2[i]
# dm2 was computed as dm2[p,q,r,s] = < p^\dagger r^\dagger s q > in the
# above. Transposing it so that it be contracted with ERIs (in Chemist's
# notation):
# E = einsum('pqrs,pqrs', eri, rdm2)
dovov = t2i.transpose(1, 0, 2) * 2 - t2i.transpose(2, 0, 1)
dovov *= 2
if moidx is None:
dm2[i, nocc:, :nocc, nocc:] = dovov
dm2[nocc:, i, nocc:, :nocc] = dovov.conj().transpose(0, 2, 1)
else:
dm2[oidx[i], vidx[:, None, None], oidx[:, None], vidx] = dovov
dm2[vidx[:, None, None], oidx[i], vidx[:, None],
oidx] = dovov.conj().transpose(0, 2, 1)
# Be careful with convention of dm1 and dm2
# dm1[q,p] = <p^\dagger q>
# dm2[p,q,r,s] = < p^\dagger r^\dagger s q >
# E = einsum('pq,qp', h1, dm1) + .5 * einsum('pqrs,pqrs', eri, dm2)
# When adding dm1 contribution, dm1 subscripts need to be flipped
for i in range(nocc0):
dm2[i, i, :, :] += dm1.T * 2
dm2[:, :, i, i] += dm1.T * 2
dm2[:, i, i, :] -= dm1.T
dm2[i, :, :, i] -= dm1
for i in range(nocc0):
for j in range(nocc0):
dm2[i, i, j, j] += 4
dm2[i, j, j, i] -= 2
return dm2 #.transpose(1,0,3,2)
def build_se_part(agf2, eri, gf_occ, gf_vir, os_factor=1.0, ss_factor=1.0):
''' Builds either the auxiliaries of the occupied self-energy,
or virtual if :attr:`gf_occ` and :attr:`gf_vir` are swapped.
Args:
eri : _ChemistsERIs
Electronic repulsion integrals
gf_occ : GreensFunction
Occupied Green's function
gf_vir : GreensFunction
Virtual Green's function
Kwargs:
os_factor : float
Opposite-spin factor for spin-component-scaled (SCS)
calculations. Default 1.0
ss_factor : float
Same-spin factor for spin-component-scaled (SCS)
calculations. Default 1.0
Returns:
:class:`SelfEnergy`
'''
cput0 = (time.clock(), time.time())
log = logger.Logger(agf2.stdout, agf2.verbose)
assert type(gf_occ) is aux.GreensFunction
assert type(gf_vir) is aux.GreensFunction
nmo = agf2.nmo
nocc = gf_occ.naux
nvir = gf_vir.naux
naux = nocc * nocc * nvir
tol = agf2.weight_tol
if not (agf2.frozen is None or agf2.frozen == 0):
mask = ragf2.get_frozen_mask(agf2)
nmo -= np.sum(~mask)
e = np.zeros((naux))
v = np.zeros((nmo, naux))
fpos = np.sqrt(0.5 * os_factor)
fneg = np.sqrt(0.5 * os_factor + ss_factor)
fdia = np.sqrt(os_factor)
eja = lib.direct_sum('j,a->ja', gf_occ.energy, -gf_vir.energy)
coeffs = (gf_occ.coupling, gf_occ.coupling, gf_vir.coupling)
qeri = _make_qmo_eris_incore(agf2, eri, coeffs)
p1 = 0
for i in range(nocc):
xija = qeri[:,i,:i].reshape(nmo, -1)
xjia = qeri[:,:i,i].reshape(nmo, -1)
xiia = qeri[:,i,i].reshape(nmo, -1)
eija = gf_occ.energy[i] + eja[:i+1]
p0, p1 = p1, p1 + i*nvir
e[p0:p1] = eija[:i].ravel()
v[:,p0:p1] = fneg * (xija - xjia)
p0, p1 = p1, p1 + i*nvir
e[p0:p1] = eija[:i].ravel()
v[:,p0:p1] = fpos * (xija + xjia)
p0, p1 = p1, p1 + nvir
e[p0:p1] = eija[i].ravel()
v[:,p0:p1] = fdia * xiia
se = aux.SelfEnergy(e, v, chempot=gf_occ.chempot)
se.remove_uncoupled(tol=tol)
if not (agf2.frozen is None or agf2.frozen == 0):
coupling = np.zeros((agf2.nmo, se.naux))
coupling[mask] = se.coupling
se = aux.SelfEnergy(se.energy, coupling, chempot=se.chempot)
log.timer('se part', *cput0)
return se