def __init__(self, cc, mo_coeff=None, method='incore'):
cput0 = (time.clock(), time.time())
moidx = numpy.ones(cc.mo_energy.size, dtype=numpy.bool)
if isinstance(cc.frozen, (int, numpy.integer)):
moidx[:cc.frozen] = False
elif len(cc.frozen) > 0:
moidx[numpy.asarray(cc.frozen)] = False
if mo_coeff is None:
self.mo_coeff = mo_coeff = cc.mo_coeff[:,moidx]
self.fock = numpy.diag(cc.mo_energy[moidx])
else: # If mo_coeff is not canonical orbital
self.mo_coeff = mo_coeff = mo_coeff[:,moidx]
dm = cc._scf.make_rdm1(cc.mo_coeff, cc.mo_occ)
fockao = cc._scf.get_hcore() + cc._scf.get_veff(cc.mol, dm)
self.fock = reduce(numpy.dot, (mo_coeff.T, fockao, mo_coeff))
nocc = cc.nocc()
nmo = cc.nmo()
nvir = nmo - nocc
mem_incore, mem_outcore, mem_basic = _mem_usage(nocc, nvir)
mem_now = pyscf.lib.current_memory()[0]
log = logger.Logger(cc.stdout, cc.verbose)
if (method == 'incore' and cc._scf._eri is not None and
(mem_incore+mem_now < cc.max_memory) or cc.mol.incore_anyway):
eri1 = pyscf.ao2mo.incore.full(cc._scf._eri, mo_coeff)
#:eri1 = pyscf.ao2mo.restore(1, eri1, nmo)
#:self.oooo = eri1[:nocc,:nocc,:nocc,:nocc].copy()
#:self.ooov = eri1[:nocc,:nocc,:nocc,nocc:].copy()
#:self.ovoo = eri1[:nocc,nocc:,:nocc,:nocc].copy()
#:self.oovv = eri1[:nocc,:nocc,nocc:,nocc:].copy()
#:self.ovov = eri1[:nocc,nocc:,:nocc,nocc:].copy()
#:ovvv = eri1[:nocc,nocc:,nocc:,nocc:].copy()
#:self.ovvv = numpy.empty((nocc,nvir,nvir*(nvir+1)//2))
#:for i in range(nocc):
#: for j in range(nvir):
#: self.ovvv[i,j] = lib.pack_tril(ovvv[i,j])
#:self.vvvv = pyscf.ao2mo.restore(4, eri1[nocc:,nocc:,nocc:,nocc:], nvir)
nvir_pair = nvir * (nvir+1) // 2
self.oooo = numpy.empty((nocc,nocc,nocc,nocc))
self.ooov = numpy.empty((nocc,nocc,nocc,nvir))
self.ovoo = numpy.empty((nocc,nvir,nocc,nocc))
self.oovv = numpy.empty((nocc,nocc,nvir,nvir))
self.ovov = numpy.empty((nocc,nvir,nocc,nvir))
self.ovvv = numpy.empty((nocc,nvir,nvir_pair))
self.vvvv = numpy.empty((nvir_pair,nvir_pair))
ij = 0
outbuf = numpy.empty((nmo,nmo,nmo))
for i in range(nocc):
buf = _ccsd.unpack_tril(eri1[ij:ij+i+1], out=outbuf[:i+1])
for j in range(i+1):
self.oooo[i,j] = self.oooo[j,i] = buf[j,:nocc,:nocc]
self.ooov[i,j] = self.ooov[j,i] = buf[j,:nocc,nocc:]
self.oovv[i,j] = self.oovv[j,i] = buf[j,nocc:,nocc:]
ij += i + 1
ij1 = 0
for i in range(nocc,nmo):
buf = _ccsd.unpack_tril(eri1[ij:ij+i+1], out=outbuf[:i+1])
self.ovoo[:,i-nocc] = buf[:nocc,:nocc,:nocc]
self.ovov[:,i-nocc] = buf[:nocc,:nocc,nocc:]
for j in range(nocc):
self.ovvv[j,i-nocc] = lib.pack_tril(_cp(buf[j,nocc:,nocc:]))
for j in range(nocc, i+1):
self.vvvv[ij1] = lib.pack_tril(_cp(buf[j,nocc:,nocc:]))
ij1 += 1
ij += i + 1
else:
cput1 = time.clock(), time.time()
_tmpfile1 = tempfile.NamedTemporaryFile()
_tmpfile2 = tempfile.NamedTemporaryFile()
self.feri1 = h5py.File(_tmpfile1.name)
orbo = mo_coeff[:,:nocc]
orbv = mo_coeff[:,nocc:]
nvpair = nvir * (nvir+1) // 2
self.oooo = self.feri1.create_dataset('oooo', (nocc,nocc,nocc,nocc), 'f8')
self.ooov = self.feri1.create_dataset('ooov', (nocc,nocc,nocc,nvir), 'f8')
self.ovoo = self.feri1.create_dataset('ovoo', (nocc,nvir,nocc,nocc), 'f8')
self.oovv = self.feri1.create_dataset('oovv', (nocc,nocc,nvir,nvir), 'f8')
self.ovov = self.feri1.create_dataset('ovov', (nocc,nvir,nocc,nvir), 'f8')
self.ovvv = self.feri1.create_dataset('ovvv', (nocc,nvir,nvpair), 'f8')
self.feri2 = h5py.File(_tmpfile2.name, 'w')
pyscf.ao2mo.full(cc.mol, orbv, self.feri2, verbose=log)
self.vvvv = self.feri2['eri_mo']
cput1 = log.timer_debug1('transforming vvvv', *cput1)
tmpfile3 = tempfile.NamedTemporaryFile()
with h5py.File(tmpfile3.name, 'w') as feri:
pyscf.ao2mo.general(cc.mol, (orbo,mo_coeff,mo_coeff,mo_coeff),
feri, verbose=log)
cput1 = log.timer_debug1('transforming oppp', *cput1)
eri1 = feri['eri_mo']
outbuf = numpy.empty((nmo,nmo,nmo))
for i in range(nocc):
buf = _ccsd.unpack_tril(_cp(eri1[i*nmo:(i+1)*nmo]), out=outbuf)
self.oooo[i] = buf[:nocc,:nocc,:nocc]
self.ooov[i] = buf[:nocc,:nocc,nocc:]
self.ovoo[i] = buf[nocc:,:nocc,:nocc]
self.oovv[i] = buf[:nocc,nocc:,nocc:]
self.ovov[i] = buf[nocc:,:nocc,nocc:]
self.ovvv[i] = _ccsd.pack_tril(_cp(buf[nocc:,nocc:,nocc:]))
cput1 = log.timer_debug1('sorting %d'%i, *cput1)
for key in feri.keys():
del(feri[key])
log.timer('CCSD integral transformation', *cput0)
def gamma2_incore(mycc, t1, t2, l1, l2):
log = logger.Logger(mycc.stdout, mycc.verbose)
nocc, nvir = t1.shape
nov = nocc * nvir
time1 = time.clock(), time.time()
#:theta = make_theta(t2)
#:mOvOv = numpy.einsum('ikca,jkcb->jbia', l2, t2)
#:mOVov = -numpy.einsum('ikca,jkbc->jbia', l2, t2)
#:mOVov += numpy.einsum('ikac,jkbc->jbia', l2, theta)
l2a = numpy.empty((nocc,nvir,nocc,nvir))
t2a = numpy.empty((nocc,nvir,nocc,nvir))
for i in range(nocc):
l2a[i] = l2[i].transpose(2,0,1)
t2a[i] = t2[i].transpose(2,0,1)
mOvOv = lib.dot(t2a.reshape(-1,nov), l2a.reshape(-1,nov).T).reshape(nocc,nvir,nocc,nvir)
for i in range(nocc):
t2a[i] = t2[i].transpose(1,0,2)
mOVov = lib.dot(t2a.reshape(-1,nov), l2a.reshape(-1,nov).T, -1).reshape(nocc,nvir,nocc,nvir)
theta = t2a
for i in range(nocc):
l2a[i] = l2[i].transpose(1,0,2)
theta[i] *= 2
theta[i] -= t2[i].transpose(2,0,1)
lib.dot(theta.reshape(-1,nov), l2a.reshape(nov,-1).T, 1, mOVov.reshape(nov,-1), 1)
theta = l2a = t2a = None
moo =(numpy.einsum('jdld->jl', mOvOv) * 2
+ numpy.einsum('jdld->jl', mOVov))
mvv =(numpy.einsum('lbld->bd', mOvOv) * 2
+ numpy.einsum('lbld->bd', mOVov))
mia =(numpy.einsum('kc,ikac->ia', l1, t2) * 2
- numpy.einsum('kc,ikca->ia', l1, t2))
mab = numpy.einsum('kc,kb->cb', l1, t1)
mij = numpy.einsum('kc,jc->jk', l1, t1) + moo*.5
gooov = numpy.zeros((nocc,nocc,nocc,nvir))
tau = _ccsd.make_tau(t2, t1, t1)
#:goooo = numpy.einsum('ijab,klab->klij', l2, tau)*.5
goooo = lib.dot(tau.reshape(-1,nvir**2), l2.reshape(-1,nvir**2).T, .5)
goooo = goooo.reshape(-1,nocc,nocc,nocc)
doooo = _cp(make_theta(goooo).transpose(0,2,1,3))
#:gooov -= numpy.einsum('ib,kjab->jkia', l1, tau)
#:gooov -= numpy.einsum('kjab,ib->jkia', l2, t1)
#:gooov += numpy.einsum('jkil,la->jkia', goooo, t1*2)
gooov = lib.dot(_cp(tau.reshape(-1,nvir)), l1.T, -1)
lib.dot(_cp(l2.reshape(-1,nvir)), t1.T, -1, gooov, 1)
gooov = gooov.reshape(nocc,nocc,nvir,nocc)
tmp = numpy.einsum('ji,ka->jkia', moo*-.5, t1)
tmp += gooov.transpose(1,0,3,2)
gooov, tmp = tmp, None
lib.dot(goooo.reshape(-1,nocc), t1, 2, gooov.reshape(-1,nvir), 1)
goovv = numpy.einsum('ia,jb->ijab', mia, t1)
for i in range(nocc):
goovv[i] += .5 * l2 [i]
goovv[i] += .5 * tau[i]
#:goovv -= numpy.einsum('jk,kiba->jiba', mij, tau)
lib.dot(mij, tau.reshape(nocc,-1), -1, goovv.reshape(nocc,-1), 1)
#:goovv -= numpy.einsum('cb,ijac->ijab', mab, t2)
#:goovv -= numpy.einsum('bd,ijad->ijab', mvv*.5, tau)
lib.dot(t2.reshape(-1,nvir), mab, -1, goovv.reshape(-1,nvir), 1)
lib.dot(tau.reshape(-1,nvir), mvv.T, -.5, goovv.reshape(-1,nvir), 1)
tau = None
#:gooov += numpy.einsum('jaic,kc->jkia', mOvOv, t1)
#:gooov -= numpy.einsum('kaic,jc->jkia', mOVov, t1)
tmp = lib.dot(mOvOv.reshape(-1,nvir), t1.T).reshape(nocc,-1,nocc,nocc)
gooov += tmp.transpose(0,3,2,1)
lib.dot(t1, mOVov.reshape(-1,nvir).T, 1, tmp.reshape(nocc,-1), 0)
gooov -= tmp.reshape(nocc,nocc,nvir,nocc).transpose(0,1,3,2)
dooov = gooov.transpose(0,2,1,3)*2 - gooov.transpose(1,2,0,3)
gooov = None
#:tmp = numpy.einsum('ikac,jc->jaik', l2, t1)
#:gOvVo -= numpy.einsum('jaik,kb->jabi', tmp, t1)
#:gOvvO = numpy.einsum('jaki,kb->jabi', tmp, t1) + mOvOv.transpose(0,3,1,2)
tmp = tmp.reshape(nocc,nocc,nocc,nvir)
lib.dot(t1, l2.reshape(-1,nvir).T, 1, tmp.reshape(nocc,-1))
gOvVo = numpy.einsum('ia,jb->jabi', l1, t1)
gOvvO = numpy.empty((nocc,nvir,nvir,nocc))
for i in range(nocc):
gOvVo[i] -= lib.dot(_cp(tmp[i].transpose(0,2,1).reshape(-1,nocc)),
t1).reshape(nocc,nvir,-1).transpose(1,2,0)
gOvVo[i] += mOVov[i].transpose(2,0,1)
gOvvO[i] = lib.dot(tmp[i].reshape(nocc,-1).T,
t1).reshape(nocc,nvir,-1).transpose(1,2,0)
gOvvO[i] += mOvOv[i].transpose(2,0,1)
tmp = None
dovvo = numpy.empty((nocc,nvir,nvir,nocc))
doovv = numpy.empty((nocc,nocc,nvir,nvir))
for i in range(nocc):
tmp = gOvVo[i] * 2 + gOvvO[i]
dovvo[i] = tmp.transpose(1,0,2)
tmp = gOvvO[i] * -2 - gOvVo[i]
doovv[i] = tmp.transpose(2,0,1)
gOvvO = gOvVo = None
tau2 = _ccsd.make_tau(t2, t1, t1)
#:goovv += numpy.einsum('ijkl,klab->ijab', goooo[:,:,j0:j1], tau2)
lib.dot(goooo.reshape(nocc*nocc,-1),
tau2.reshape(-1,nvir**2), 1, goovv.reshape(-1,nvir**2), 1)
tau2 += numpy.einsum('ia,jb->ijab', t1, t1)
tau2p = tau2.reshape(nocc,nvir,nocc,nvir)
for i in range(nocc):
tau2p[i] = tau2[i].transpose(2,0,1)
tau2, tau2p = tau2p.reshape(nov,-1), None
#:goovv += numpy.einsum('ibld,jlda->ijab', mOvOv, tau2) * .5
#:goovv -= numpy.einsum('iald,jldb->ijab', mOVov, tau2) * .5
tmp = lib.dot(mOvOv.reshape(-1,nov), tau2.T, .5).reshape(nocc,nvir,-1,nvir)
for i in range(nocc):
tmp[i] = goovv[i].transpose(1,0,2) + tmp[i].transpose(2,1,0)
goovv, tmp = tmp, None
lib.dot(mOVov.reshape(-1,nov), tau2.T, -.5, goovv.reshape(nov,-1), 1)
#:goovv += numpy.einsum('iald,jlbd->ijab', mOVov*2+mOvOv, t2) * .5
t2a, tau2 = tau2.reshape(nocc,nvir,nocc,nvir), None
for i in range(nocc):
t2a[i] = t2[i].transpose(1,0,2)
tmp = mOVov*2
tmp += mOvOv
lib.dot(tmp.reshape(-1,nov), t2a.reshape(nov,-1), .5, goovv.reshape(nov,-1), 1)
t2a = tmp = None
for i in range(nocc):
goovv[i] = goovv[i] * 2 - goovv[i].transpose(2,1,0)
dovov = goovv
goooo = goovv = None
#:gvovv += numpy.einsum('aick,kb->aibc', pvOVo, t1)
mOVov = lib.transpose(mOVov.reshape(nov,-1))
gvovv = lib.dot(mOVov.reshape(nocc,-1).T, t1).reshape(nvir,nocc,nvir,nvir)
mOVov = None
tmp = numpy.einsum('ja,jb->ab', l1, t1)
#:gvovv += numpy.einsum('ab,ic->aibc', tmp, t1)
#:gvovv += numpy.einsum('ba,ic->aibc', mvv, t1*.5)
for i in range(nvir):
gvovv[i] += numpy.einsum('b,ic->icb', tmp[i], t1)
gvovv[i] += numpy.einsum('b,ic->icb', mvv[:,i]*.5, t1)
gvovv[i] = gvovv[i].transpose(0,2,1)
#:gvovv += numpy.einsum('ja,jibc->aibc', l1, t2)
#:gvovv += numpy.einsum('jibc,ja->aibc', l2, t1)
#:gvovv -= numpy.einsum('aibk,kc->aibc', pvOvO, t1)
mOvOv = lib.transpose(mOvOv.reshape(nov,-1))
lib.dot(mOvOv.reshape(nocc,-1).T, t1, -1, gvovv.reshape(-1,nvir), 1)
mOvOv = None
lib.dot(l1.T, t2.reshape(nocc,-1), 1, gvovv.reshape(nvir,-1), 1)
lib.dot(t1.T, l2.reshape(nocc,-1), 1, gvovv.reshape(nvir,-1), 1)
tmp = numpy.empty((nocc,nvir,nvir))
for i in range(nvir):
#:gvovv*2 - gvovv.transpose(0,1,3,2)
gvovv[i] = _ccsd.make_021(gvovv[i], gvovv[i], 2, -1, out=tmp)
#:gvvvv = numpy.einsum('ijab,ijcd->abcd', l2, t2)*.5
#:jabc = numpy.einsum('ijab,ic->jabc', l2, t1) * .5
#:gvvvv += numpy.einsum('jabc,jd->abcd', jabc, t1)
#:gvovv -= numpy.einsum('adbc,id->aibc', gvvvv, t1*2)
tau = _ccsd.make_tau(t2, t1, t1)
theta = make_theta(tau)
tau = None
l2tmp = _ccsd.pack_tril(l2.reshape(-1,nvir,nvir))
gtmp = lib.dot(l2tmp.T, theta.reshape(nocc**2,-1), .5).reshape(-1,nvir,nvir)
l2tmp = theta = None
nvir_pair = nvir * (nvir+1) //2
tmp = numpy.empty((nvir,nvir,nvir))
tmp1 = numpy.empty((nvir,nvir,nvir))
tmptril = numpy.empty((nvir,nvir_pair))
diag_idx = numpy.arange(nvir)
diag_idx = diag_idx*(diag_idx+1)//2 + diag_idx
dvvvv = numpy.empty((nvir_pair,nvir_pair))
dovvv = numpy.empty((nocc,nvir,nvir,nvir))
# dvvov = (gvovv*2 - gvovv.transpose(0,1,3,2)).transpose(0,2,1,3)
# dovvv = dvvov.transpose(2,3,0,1)
p0 = 0
for i in range(nvir):
tmp[:i+1] = gtmp[p0:p0+i+1]
for j in range(i+1, nvir):
tmp[j] = gtmp[j*(j+1)//2+i].T
lib.dot(t1, tmp.reshape(nvir,-1), -2, gvovv[i].reshape(nocc,-1), 1)
dovvv[:,:,i] = gvovv[i].transpose(0,2,1)
#:gvvvv[i] = (tmp*2-tmp.transpose(0,2,1)).transpose(1,0,2)
#:gvvvv = .5*(gvvvv+gvvvv.transpose(0,1,3,2))
#:dvvvv = .5*(gvvvv+gvvvv.transpose(1,0,3,2))
tmp1[:] = tmp.transpose(1,0,2)
_ccsd.precontract(tmp1, diag_fac=2, out=tmptril)
dvvvv[p0:p0+i] += tmptril[:i]
dvvvv[p0:p0+i] *= .25
dvvvv[i*(i+1)//2+i] = tmptril[i] * .5
for j in range(i+1, nvir):
dvvvv[j*(j+1)//2+i] = tmptril[j]
p0 += i + 1
gtmp = tmp = tmp1 = tmptril = gvovv = None
dvvov = dovvv.transpose(2,3,0,1)
return (dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov)
def gamma2_incore(mycc, t1, t2, l1, l2):
log = logger.Logger(mycc.stdout, mycc.verbose)
nocc, nvir = t1.shape
nov = nocc * nvir
time1 = time.clock(), time.time()
#:theta = make_theta(t2)
#:mOvOv = numpy.einsum('ikca,jkcb->jbia', l2, t2)
#:mOVov = -numpy.einsum('ikca,jkbc->jbia', l2, t2)
#:mOVov += numpy.einsum('ikac,jkbc->jbia', l2, theta)
l2a = numpy.empty((nocc, nvir, nocc, nvir))
t2a = numpy.empty((nocc, nvir, nocc, nvir))
for i in range(nocc):
l2a[i] = l2[i].transpose(2, 0, 1)
t2a[i] = t2[i].transpose(2, 0, 1)
mOvOv = lib.dot(t2a.reshape(-1, nov),
l2a.reshape(-1, nov).T).reshape(nocc, nvir, nocc, nvir)
for i in range(nocc):
t2a[i] = t2[i].transpose(1, 0, 2)
mOVov = lib.dot(t2a.reshape(-1, nov),
l2a.reshape(-1, nov).T,
-1).reshape(nocc, nvir, nocc, nvir)
theta = t2a
for i in range(nocc):
l2a[i] = l2[i].transpose(1, 0, 2)
theta[i] *= 2
theta[i] -= t2[i].transpose(2, 0, 1)
lib.dot(theta.reshape(-1, nov),
l2a.reshape(nov, -1).T, 1, mOVov.reshape(nov, -1), 1)
theta = l2a = t2a = None
moo = (numpy.einsum('jdld->jl', mOvOv) * 2 +
numpy.einsum('jdld->jl', mOVov))
mvv = (numpy.einsum('lbld->bd', mOvOv) * 2 +
numpy.einsum('lbld->bd', mOVov))
mia = (numpy.einsum('kc,ikac->ia', l1, t2) * 2 -
numpy.einsum('kc,ikca->ia', l1, t2))
mab = numpy.einsum('kc,kb->cb', l1, t1)
mij = numpy.einsum('kc,jc->jk', l1, t1) + moo * .5
gooov = numpy.zeros((nocc, nocc, nocc, nvir))
tau = _ccsd.make_tau(t2, t1, t1)
#:goooo = numpy.einsum('ijab,klab->klij', l2, tau)*.5
goooo = lib.dot(tau.reshape(-1, nvir**2), l2.reshape(-1, nvir**2).T, .5)
goooo = goooo.reshape(-1, nocc, nocc, nocc)
doooo = _cp(make_theta(goooo).transpose(0, 2, 1, 3))
#:gooov -= numpy.einsum('ib,kjab->jkia', l1, tau)
#:gooov -= numpy.einsum('kjab,ib->jkia', l2, t1)
#:gooov += numpy.einsum('jkil,la->jkia', goooo, t1*2)
gooov = lib.dot(_cp(tau.reshape(-1, nvir)), l1.T, -1)
lib.dot(_cp(l2.reshape(-1, nvir)), t1.T, -1, gooov, 1)
gooov = gooov.reshape(nocc, nocc, nvir, nocc)
tmp = numpy.einsum('ji,ka->jkia', moo * -.5, t1)
tmp += gooov.transpose(1, 0, 3, 2)
gooov, tmp = tmp, None
lib.dot(goooo.reshape(-1, nocc), t1, 2, gooov.reshape(-1, nvir), 1)
goovv = numpy.einsum('ia,jb->ijab', mia, t1)
for i in range(nocc):
goovv[i] += .5 * l2[i]
goovv[i] += .5 * tau[i]
#:goovv -= numpy.einsum('jk,kiba->jiba', mij, tau)
lib.dot(mij, tau.reshape(nocc, -1), -1, goovv.reshape(nocc, -1), 1)
#:goovv -= numpy.einsum('cb,ijac->ijab', mab, t2)
#:goovv -= numpy.einsum('bd,ijad->ijab', mvv*.5, tau)
lib.dot(t2.reshape(-1, nvir), mab, -1, goovv.reshape(-1, nvir), 1)
lib.dot(tau.reshape(-1, nvir), mvv.T, -.5, goovv.reshape(-1, nvir), 1)
tau = None
#:gooov += numpy.einsum('jaic,kc->jkia', mOvOv, t1)
#:gooov -= numpy.einsum('kaic,jc->jkia', mOVov, t1)
tmp = lib.dot(mOvOv.reshape(-1, nvir), t1.T).reshape(nocc, -1, nocc, nocc)
gooov += tmp.transpose(0, 3, 2, 1)
lib.dot(t1, mOVov.reshape(-1, nvir).T, 1, tmp.reshape(nocc, -1), 0)
gooov -= tmp.reshape(nocc, nocc, nvir, nocc).transpose(0, 1, 3, 2)
dooov = gooov.transpose(0, 2, 1, 3) * 2 - gooov.transpose(1, 2, 0, 3)
gooov = None
#:tmp = numpy.einsum('ikac,jc->jaik', l2, t1)
#:gOvVo -= numpy.einsum('jaik,kb->jabi', tmp, t1)
#:gOvvO = numpy.einsum('jaki,kb->jabi', tmp, t1) + mOvOv.transpose(0,3,1,2)
tmp = tmp.reshape(nocc, nocc, nocc, nvir)
lib.dot(t1, l2.reshape(-1, nvir).T, 1, tmp.reshape(nocc, -1))
gOvVo = numpy.einsum('ia,jb->jabi', l1, t1)
gOvvO = numpy.empty((nocc, nvir, nvir, nocc))
for i in range(nocc):
gOvVo[i] -= lib.dot(_cp(tmp[i].transpose(0, 2, 1).reshape(-1, nocc)),
t1).reshape(nocc, nvir, -1).transpose(1, 2, 0)
gOvVo[i] += mOVov[i].transpose(2, 0, 1)
gOvvO[i] = lib.dot(tmp[i].reshape(nocc, -1).T,
t1).reshape(nocc, nvir, -1).transpose(1, 2, 0)
gOvvO[i] += mOvOv[i].transpose(2, 0, 1)
tmp = None
dovvo = numpy.empty((nocc, nvir, nvir, nocc))
doovv = numpy.empty((nocc, nocc, nvir, nvir))
for i in range(nocc):
tmp = gOvVo[i] * 2 + gOvvO[i]
dovvo[i] = tmp.transpose(1, 0, 2)
tmp = gOvvO[i] * -2 - gOvVo[i]
doovv[i] = tmp.transpose(2, 0, 1)
gOvvO = gOvVo = None
tau2 = _ccsd.make_tau(t2, t1, t1)
#:goovv += numpy.einsum('ijkl,klab->ijab', goooo[:,:,j0:j1], tau2)
lib.dot(goooo.reshape(nocc * nocc, -1), tau2.reshape(-1, nvir**2), 1,
goovv.reshape(-1, nvir**2), 1)
tau2 += numpy.einsum('ia,jb->ijab', t1, t1)
tau2p = tau2.reshape(nocc, nvir, nocc, nvir)
for i in range(nocc):
tau2p[i] = tau2[i].transpose(2, 0, 1)
tau2, tau2p = tau2p.reshape(nov, -1), None
#:goovv += numpy.einsum('ibld,jlda->ijab', mOvOv, tau2) * .5
#:goovv -= numpy.einsum('iald,jldb->ijab', mOVov, tau2) * .5
tmp = lib.dot(mOvOv.reshape(-1, nov), tau2.T,
.5).reshape(nocc, nvir, -1, nvir)
for i in range(nocc):
tmp[i] = goovv[i].transpose(1, 0, 2) + tmp[i].transpose(2, 1, 0)
goovv, tmp = tmp, None
lib.dot(mOVov.reshape(-1, nov), tau2.T, -.5, goovv.reshape(nov, -1), 1)
#:goovv += numpy.einsum('iald,jlbd->ijab', mOVov*2+mOvOv, t2) * .5
t2a, tau2 = tau2.reshape(nocc, nvir, nocc, nvir), None
for i in range(nocc):
t2a[i] = t2[i].transpose(1, 0, 2)
tmp = mOVov * 2
tmp += mOvOv
lib.dot(tmp.reshape(-1, nov), t2a.reshape(nov, -1), .5,
goovv.reshape(nov, -1), 1)
t2a = tmp = None
for i in range(nocc):
goovv[i] = goovv[i] * 2 - goovv[i].transpose(2, 1, 0)
dovov = goovv
goooo = goovv = None
#:gvovv += numpy.einsum('aick,kb->aibc', pvOVo, t1)
mOVov = lib.transpose(mOVov.reshape(nov, -1))
gvovv = lib.dot(mOVov.reshape(nocc, -1).T,
t1).reshape(nvir, nocc, nvir, nvir)
mOVov = None
tmp = numpy.einsum('ja,jb->ab', l1, t1)
#:gvovv += numpy.einsum('ab,ic->aibc', tmp, t1)
#:gvovv += numpy.einsum('ba,ic->aibc', mvv, t1*.5)
for i in range(nvir):
gvovv[i] += numpy.einsum('b,ic->icb', tmp[i], t1)
gvovv[i] += numpy.einsum('b,ic->icb', mvv[:, i] * .5, t1)
gvovv[i] = gvovv[i].transpose(0, 2, 1)
#:gvovv += numpy.einsum('ja,jibc->aibc', l1, t2)
#:gvovv += numpy.einsum('jibc,ja->aibc', l2, t1)
#:gvovv -= numpy.einsum('aibk,kc->aibc', pvOvO, t1)
mOvOv = lib.transpose(mOvOv.reshape(nov, -1))
lib.dot(mOvOv.reshape(nocc, -1).T, t1, -1, gvovv.reshape(-1, nvir), 1)
mOvOv = None
lib.dot(l1.T, t2.reshape(nocc, -1), 1, gvovv.reshape(nvir, -1), 1)
lib.dot(t1.T, l2.reshape(nocc, -1), 1, gvovv.reshape(nvir, -1), 1)
tmp = numpy.empty((nocc, nvir, nvir))
for i in range(nvir):
#:gvovv*2 - gvovv.transpose(0,1,3,2)
gvovv[i] = _ccsd.make_021(gvovv[i], gvovv[i], 2, -1, out=tmp)
#:gvvvv = numpy.einsum('ijab,ijcd->abcd', l2, t2)*.5
#:jabc = numpy.einsum('ijab,ic->jabc', l2, t1) * .5
#:gvvvv += numpy.einsum('jabc,jd->abcd', jabc, t1)
#:gvovv -= numpy.einsum('adbc,id->aibc', gvvvv, t1*2)
tau = _ccsd.make_tau(t2, t1, t1)
theta = make_theta(tau)
tau = None
l2tmp = _ccsd.pack_tril(l2.reshape(-1, nvir, nvir))
gtmp = lib.dot(l2tmp.T, theta.reshape(nocc**2, -1),
.5).reshape(-1, nvir, nvir)
l2tmp = theta = None
nvir_pair = nvir * (nvir + 1) // 2
tmp = numpy.empty((nvir, nvir, nvir))
tmp1 = numpy.empty((nvir, nvir, nvir))
tmptril = numpy.empty((nvir, nvir_pair))
diag_idx = numpy.arange(nvir)
diag_idx = diag_idx * (diag_idx + 1) // 2 + diag_idx
dvvvv = numpy.empty((nvir_pair, nvir_pair))
dovvv = numpy.empty((nocc, nvir, nvir, nvir))
# dvvov = (gvovv*2 - gvovv.transpose(0,1,3,2)).transpose(0,2,1,3)
# dovvv = dvvov.transpose(2,3,0,1)
p0 = 0
for i in range(nvir):
tmp[:i + 1] = gtmp[p0:p0 + i + 1]
for j in range(i + 1, nvir):
tmp[j] = gtmp[j * (j + 1) // 2 + i].T
lib.dot(t1, tmp.reshape(nvir, -1), -2, gvovv[i].reshape(nocc, -1), 1)
dovvv[:, :, i] = gvovv[i].transpose(0, 2, 1)
#:gvvvv[i] = (tmp*2-tmp.transpose(0,2,1)).transpose(1,0,2)
#:gvvvv = .5*(gvvvv+gvvvv.transpose(0,1,3,2))
#:dvvvv = .5*(gvvvv+gvvvv.transpose(1,0,3,2))
tmp1[:] = tmp.transpose(1, 0, 2)
_ccsd.precontract(tmp1, diag_fac=2, out=tmptril)
dvvvv[p0:p0 + i] += tmptril[:i]
dvvvv[p0:p0 + i] *= .25
dvvvv[i * (i + 1) // 2 + i] = tmptril[i] * .5
for j in range(i + 1, nvir):
dvvvv[j * (j + 1) // 2 + i] = tmptril[j]
p0 += i + 1
gtmp = tmp = tmp1 = tmptril = gvovv = None
dvvov = dovvv.transpose(2, 3, 0, 1)
return (dovov, dvvvv, doooo, doovv, dovvo, dvvov, dovvv, dooov)
def __init__(self, cc, mo_coeff=None, method='incore'):
cput0 = (time.clock(), time.time())
moidx = numpy.ones(cc.mo_energy.size, dtype=numpy.bool)
if isinstance(cc.frozen, (int, numpy.integer)):
moidx[:cc.frozen] = False
elif len(cc.frozen) > 0:
moidx[numpy.asarray(cc.frozen)] = False
if mo_coeff is None:
self.mo_coeff = mo_coeff = cc.mo_coeff[:, moidx]
self.fock = numpy.diag(cc.mo_energy[moidx])
else: # If mo_coeff is not canonical orbital
self.mo_coeff = mo_coeff = mo_coeff[:, moidx]
dm = cc._scf.make_rdm1(cc.mo_coeff, cc.mo_occ)
fockao = cc._scf.get_hcore() + cc._scf.get_veff(cc.mol, dm)
self.fock = reduce(numpy.dot, (mo_coeff.T, fockao, mo_coeff))
nocc = cc.nocc()
nmo = cc.nmo()
nvir = nmo - nocc
mem_incore, mem_outcore, mem_basic = _mem_usage(nocc, nvir)
mem_now = pyscf.lib.current_memory()[0]
log = logger.Logger(cc.stdout, cc.verbose)
if (method == 'incore' and cc._scf._eri is not None and
(mem_incore + mem_now < cc.max_memory) or cc.mol.incore_anyway):
eri1 = pyscf.ao2mo.incore.full(cc._scf._eri, mo_coeff)
#:eri1 = pyscf.ao2mo.restore(1, eri1, nmo)
#:self.oooo = eri1[:nocc,:nocc,:nocc,:nocc].copy()
#:self.ooov = eri1[:nocc,:nocc,:nocc,nocc:].copy()
#:self.ovoo = eri1[:nocc,nocc:,:nocc,:nocc].copy()
#:self.oovv = eri1[:nocc,:nocc,nocc:,nocc:].copy()
#:self.ovov = eri1[:nocc,nocc:,:nocc,nocc:].copy()
#:ovvv = eri1[:nocc,nocc:,nocc:,nocc:].copy()
#:self.ovvv = numpy.empty((nocc,nvir,nvir*(nvir+1)//2))
#:for i in range(nocc):
#: for j in range(nvir):
#: self.ovvv[i,j] = lib.pack_tril(ovvv[i,j])
#:self.vvvv = pyscf.ao2mo.restore(4, eri1[nocc:,nocc:,nocc:,nocc:], nvir)
nvir_pair = nvir * (nvir + 1) // 2
self.oooo = numpy.empty((nocc, nocc, nocc, nocc))
self.ooov = numpy.empty((nocc, nocc, nocc, nvir))
self.ovoo = numpy.empty((nocc, nvir, nocc, nocc))
self.oovv = numpy.empty((nocc, nocc, nvir, nvir))
self.ovov = numpy.empty((nocc, nvir, nocc, nvir))
self.ovvv = numpy.empty((nocc, nvir, nvir_pair))
self.vvvv = numpy.empty((nvir_pair, nvir_pair))
ij = 0
outbuf = numpy.empty((nmo, nmo, nmo))
for i in range(nocc):
buf = _ccsd.unpack_tril(eri1[ij:ij + i + 1],
out=outbuf[:i + 1])
for j in range(i + 1):
self.oooo[i, j] = self.oooo[j, i] = buf[j, :nocc, :nocc]
self.ooov[i, j] = self.ooov[j, i] = buf[j, :nocc, nocc:]
self.oovv[i, j] = self.oovv[j, i] = buf[j, nocc:, nocc:]
ij += i + 1
ij1 = 0
for i in range(nocc, nmo):
buf = _ccsd.unpack_tril(eri1[ij:ij + i + 1],
out=outbuf[:i + 1])
self.ovoo[:, i - nocc] = buf[:nocc, :nocc, :nocc]
self.ovov[:, i - nocc] = buf[:nocc, :nocc, nocc:]
for j in range(nocc):
self.ovvv[j, i - nocc] = lib.pack_tril(
_cp(buf[j, nocc:, nocc:]))
for j in range(nocc, i + 1):
self.vvvv[ij1] = lib.pack_tril(_cp(buf[j, nocc:, nocc:]))
ij1 += 1
ij += i + 1
else:
cput1 = time.clock(), time.time()
_tmpfile1 = tempfile.NamedTemporaryFile()
_tmpfile2 = tempfile.NamedTemporaryFile()
self.feri1 = h5py.File(_tmpfile1.name)
orbo = mo_coeff[:, :nocc]
orbv = mo_coeff[:, nocc:]
nvpair = nvir * (nvir + 1) // 2
self.oooo = self.feri1.create_dataset('oooo',
(nocc, nocc, nocc, nocc),
'f8')
self.ooov = self.feri1.create_dataset('ooov',
(nocc, nocc, nocc, nvir),
'f8')
self.ovoo = self.feri1.create_dataset('ovoo',
(nocc, nvir, nocc, nocc),
'f8')
self.oovv = self.feri1.create_dataset('oovv',
(nocc, nocc, nvir, nvir),
'f8')
self.ovov = self.feri1.create_dataset('ovov',
(nocc, nvir, nocc, nvir),
'f8')
self.ovvv = self.feri1.create_dataset('ovvv', (nocc, nvir, nvpair),
'f8')
max_memory = max(2000,
cc.max_memory - pyscf.lib.current_memory()[0])
self.feri2 = h5py.File(_tmpfile2.name, 'w')
pyscf.ao2mo.full(cc.mol,
orbv,
self.feri2,
max_memory=max_memory,
verbose=log)
self.vvvv = self.feri2['eri_mo']
cput1 = log.timer_debug1('transforming vvvv', *cput1)
tmpfile3 = tempfile.NamedTemporaryFile()
with h5py.File(tmpfile3.name, 'w') as feri:
max_memory = max(2000,
cc.max_memory - pyscf.lib.current_memory()[0])
pyscf.ao2mo.general(cc.mol,
(orbo, mo_coeff, mo_coeff, mo_coeff),
feri,
max_memory=max_memory,
verbose=log)
cput1 = log.timer_debug1('transforming oppp', *cput1)
eri1 = feri['eri_mo']
outbuf = numpy.empty((nmo, nmo, nmo))
for i in range(nocc):
buf = _ccsd.unpack_tril(_cp(eri1[i * nmo:(i + 1) * nmo]),
out=outbuf)
self.oooo[i] = buf[:nocc, :nocc, :nocc]
self.ooov[i] = buf[:nocc, :nocc, nocc:]
self.ovoo[i] = buf[nocc:, :nocc, :nocc]
self.oovv[i] = buf[:nocc, nocc:, nocc:]
self.ovov[i] = buf[nocc:, :nocc, nocc:]
self.ovvv[i] = _ccsd.pack_tril(
_cp(buf[nocc:, nocc:, nocc:]))
cput1 = log.timer_debug1('sorting %d' % i, *cput1)
for key in feri.keys():
del (feri[key])
log.timer('CCSD integral transformation', *cput0)
