def _make_eris_outcore(mycc, mo_coeff=None):
cput0 = (logger.process_clock(), logger.perf_counter())
log = logger.Logger(mycc.stdout, mycc.verbose)
eris = _ChemistsERIs()
eris._common_init_(mycc, mo_coeff)
mol = mycc.mol
mo_coeff = eris.mo_coeff
nocc = eris.nocc
nao, nmo = mo_coeff.shape
nvir = nmo - nocc
eris.feri1 = lib.H5TmpFile()
eris.oooo = eris.feri1.create_dataset('oooo', (nocc, nocc, nocc, nocc),
'f8')
eris.ovoo = eris.feri1.create_dataset('ovoo', (nocc, nvir, nocc, nocc),
'f8',
chunks=(nocc, 1, nocc, nocc))
eris.ovov = eris.feri1.create_dataset('ovov', (nocc, nvir, nocc, nvir),
'f8',
chunks=(nocc, 1, nocc, nvir))
eris.ovvo = eris.feri1.create_dataset('ovvo', (nocc, nvir, nvir, nocc),
'f8',
chunks=(nocc, 1, nvir, nocc))
eris.ovvv = eris.feri1.create_dataset('ovvv', (nocc, nvir, nvir, nvir),
'f8')
eris.oovv = eris.feri1.create_dataset('oovv', (nocc, nocc, nvir, nvir),
'f8',
chunks=(nocc, nocc, 1, nvir))
max_memory = max(MEMORYMIN, mycc.max_memory - lib.current_memory()[0])
ftmp = lib.H5TmpFile()
ao2mo.full(mol, mo_coeff, ftmp, max_memory=max_memory, verbose=log)
eri = ftmp['eri_mo']
nocc_pair = nocc * (nocc + 1) // 2
tril2sq = lib.square_mat_in_trilu_indices(nmo)
oo = eri[:nocc_pair]
eris.oooo[:] = ao2mo.restore(1, oo[:, :nocc_pair], nocc)
oovv = lib.take_2d(oo, tril2sq[:nocc, :nocc].ravel(),
tril2sq[nocc:, nocc:].ravel())
eris.oovv[:] = oovv.reshape(nocc, nocc, nvir, nvir)
oo = oovv = None
tril2sq = lib.square_mat_in_trilu_indices(nmo)
blksize = min(nvir, max(BLKMIN, int(max_memory * 1e6 / 8 / nmo**3 / 2)))
for p0, p1 in lib.prange(0, nvir, blksize):
q0, q1 = p0 + nocc, p1 + nocc
off0 = q0 * (q0 + 1) // 2
off1 = q1 * (q1 + 1) // 2
buf = lib.unpack_tril(eri[off0:off1])
tmp = buf[tril2sq[q0:q1, :nocc] - off0]
eris.ovoo[:, p0:p1] = tmp[:, :, :nocc, :nocc].transpose(1, 0, 2, 3)
eris.ovvo[:, p0:p1] = tmp[:, :, nocc:, :nocc].transpose(1, 0, 2, 3)
eris.ovov[:, p0:p1] = tmp[:, :, :nocc, nocc:].transpose(1, 0, 2, 3)
eris.ovvv[:, p0:p1] = tmp[:, :, nocc:, nocc:].transpose(1, 0, 2, 3)
buf = tmp = None
log.timer('GW integral transformation', *cput0)
return eris
def test_add_vvVV(self):
myucc = uccsd.UCCSD(mf_s2)
nocca, noccb = 6,4
nmo = mf_s2.mo_occ[0].size
nvira, nvirb = nmo-nocca, nmo-noccb
numpy.random.seed(9)
t1 = [numpy.zeros((nocca,nvira)),
numpy.zeros((noccb,nvirb))]
t2 = [numpy.random.random((nocca,nocca,nvira,nvira))-.9,
numpy.random.random((nocca,noccb,nvira,nvirb))-.9,
numpy.random.random((noccb,noccb,nvirb,nvirb))-.9]
t2[0] = t2[0] - t2[0].transpose(1,0,2,3)
t2[0] = t2[0] - t2[0].transpose(0,1,3,2)
t2[2] = t2[2] - t2[2].transpose(1,0,2,3)
t2[2] = t2[2] - t2[2].transpose(0,1,3,2)
eris1 = copy.copy(eris)
idxa = lib.square_mat_in_trilu_indices(nvira)
idxb = lib.square_mat_in_trilu_indices(nvirb)
vvVV = eris1.vvVV[:,idxb][idxa]
ref = lib.einsum('acbd,ijcd->ijab', vvVV, t2[1])
t2a = myucc._add_vvVV((t1[0]*0,t1[1]*0), t2[1], eris)
self.assertAlmostEqual(abs(ref-t2a).max(), 0, 12)
myucc.direct = True
eris1.vvvv = None # == with_ovvv=True in the call below
eris1.VVVV = None
eris1.vvVV = None
t1 = None
myucc.mo_coeff, eris1.mo_coeff = eris1.mo_coeff, None
t2b = myucc._add_vvVV(t1, t2[1], eris1)
self.assertAlmostEqual(abs(ref-t2b).max(), 0, 12)
def test_add_vvVV(self):
myucc = uccsd.UCCSD(mf_s2)
nocca, noccb = 6, 4
nmo = mf_s2.mo_occ[0].size
nvira, nvirb = nmo - nocca, nmo - noccb
numpy.random.seed(9)
t1 = [numpy.zeros((nocca, nvira)), numpy.zeros((noccb, nvirb))]
t2 = [
numpy.random.random((nocca, nocca, nvira, nvira)) - .9,
numpy.random.random((nocca, noccb, nvira, nvirb)) - .9,
numpy.random.random((noccb, noccb, nvirb, nvirb)) - .9
]
t2[0] = t2[0] - t2[0].transpose(1, 0, 2, 3)
t2[0] = t2[0] - t2[0].transpose(0, 1, 3, 2)
t2[2] = t2[2] - t2[2].transpose(1, 0, 2, 3)
t2[2] = t2[2] - t2[2].transpose(0, 1, 3, 2)
eris1 = copy.copy(eris)
idxa = lib.square_mat_in_trilu_indices(nvira)
idxb = lib.square_mat_in_trilu_indices(nvirb)
vvVV = eris1.vvVV[:, idxb][idxa]
ref = lib.einsum('acbd,ijcd->ijab', vvVV, t2[1])
t2a = myucc._add_vvVV((t1[0] * 0, t1[1] * 0), t2[1], eris)
self.assertAlmostEqual(abs(ref - t2a).max(), 0, 12)
myucc.direct = True
eris1.vvvv = None # == with_ovvv=True in the call below
eris1.VVVV = None
eris1.vvVV = None
t1 = None
myucc.mo_coeff, eris1.mo_coeff = eris1.mo_coeff, None
t2b = myucc._add_vvVV(t1, t2[1], eris1)
self.assertAlmostEqual(abs(ref - t2b).max(), 0, 12)
def test_eris_contract_vvvv_t2(self):
mol = gto.Mole()
nocca, noccb, nvira, nvirb = 5, 4, 12, 13
nvira_pair = nvira*(nvira+1)//2
nvirb_pair = nvirb*(nvirb+1)//2
numpy.random.seed(9)
t2 = numpy.random.random((nocca,noccb,nvira,nvirb))
eris = uccsd._ChemistsERIs()
eris.vvVV = numpy.random.random((nvira_pair,nvirb_pair))
eris.mol = mol
myucc.max_memory, bak = 0, myucc.max_memory
vt2 = eris._contract_vvVV_t2(myucc, t2, eris.vvVV)
myucc.max_memory = bak
self.assertAlmostEqual(lib.finger(vt2), 12.00904827896089, 11)
idxa = lib.square_mat_in_trilu_indices(nvira)
idxb = lib.square_mat_in_trilu_indices(nvirb)
vvVV = eris.vvVV[:,idxb][idxa]
ref = lib.einsum('acbd,ijcd->ijab', vvVV, t2)
self.assertAlmostEqual(abs(vt2 - ref).max(), 0, 11)
# _contract_VVVV_t2, testing complex and real mixed contraction
VVVV =(numpy.random.random((nvirb,nvirb,nvirb,nvirb)) +
numpy.random.random((nvirb,nvirb,nvirb,nvirb))*1j - (.5+.5j))
VVVV = VVVV + VVVV.transpose(1,0,3,2).conj()
VVVV = VVVV + VVVV.transpose(2,3,0,1)
eris.VVVV = VVVV
t2 = numpy.random.random((noccb,noccb,nvirb,nvirb))
t2 = t2 - t2.transpose(0,1,3,2)
t2 = t2 - t2.transpose(1,0,3,2)
myucc.max_memory, bak = 0, myucc.max_memory
vt2 = eris._contract_VVVV_t2(myucc, t2, eris.VVVV)
myucc.max_memory = bak
self.assertAlmostEqual(lib.finger(vt2), 47.903883794299404-50.501573400833429j, 11)
ref = lib.einsum('acbd,ijcd->ijab', eris.VVVV, t2)
self.assertAlmostEqual(abs(vt2 - ref).max(), 0, 11)
def test_eris_contract_vvvv_t2(self):
mol = gto.Mole()
nocca, noccb, nvira, nvirb = 5, 4, 12, 13
nvira_pair = nvira*(nvira+1)//2
nvirb_pair = nvirb*(nvirb+1)//2
numpy.random.seed(9)
t2 = numpy.random.random((nocca,noccb,nvira,nvirb))
eris = uccsd._ChemistsERIs()
eris.vvVV = numpy.random.random((nvira_pair,nvirb_pair))
eris.mol = mol
myucc.max_memory, bak = 0, myucc.max_memory
vt2 = eris._contract_vvVV_t2(myucc, t2, eris.vvVV)
myucc.max_memory = bak
self.assertAlmostEqual(lib.finger(vt2), 12.00904827896089, 11)
idxa = lib.square_mat_in_trilu_indices(nvira)
idxb = lib.square_mat_in_trilu_indices(nvirb)
vvVV = eris.vvVV[:,idxb][idxa]
ref = lib.einsum('acbd,ijcd->ijab', vvVV, t2)
self.assertAlmostEqual(abs(vt2 - ref).max(), 0, 11)
# _contract_VVVV_t2, testing complex and real mixed contraction
VVVV =(numpy.random.random((nvirb,nvirb,nvirb,nvirb)) +
numpy.random.random((nvirb,nvirb,nvirb,nvirb))*1j - (.5+.5j))
VVVV = VVVV + VVVV.transpose(1,0,3,2).conj()
VVVV = VVVV + VVVV.transpose(2,3,0,1)
eris.VVVV = VVVV
t2 = numpy.random.random((noccb,noccb,nvirb,nvirb))
t2 = t2 - t2.transpose(0,1,3,2)
t2 = t2 - t2.transpose(1,0,3,2)
myucc.max_memory, bak = 0, myucc.max_memory
vt2 = eris._contract_VVVV_t2(myucc, t2, eris.VVVV)
myucc.max_memory = bak
self.assertAlmostEqual(lib.finger(vt2), 47.903883794299404-50.501573400833429j, 11)
ref = lib.einsum('acbd,ijcd->ijab', eris.VVVV, t2)
self.assertAlmostEqual(abs(vt2 - ref).max(), 0, 11)
def _make_eris_outcore(mycc, mo_coeff=None):
cput0 = (time.clock(), time.time())
log = logger.Logger(mycc.stdout, mycc.verbose)
eris = _ChemistsERIs()
eris._common_init_(mycc, mo_coeff)
mol = mycc.mol
mo_coeff = eris.mo_coeff
nocc = eris.nocc
nao, nmo = mo_coeff.shape
nvir = nmo - nocc
orbo = mo_coeff[:,:nocc]
orbv = mo_coeff[:,nocc:]
nvpair = nvir * (nvir+1) // 2
eris.feri1 = lib.H5TmpFile()
eris.oooo = eris.feri1.create_dataset('oooo', (nocc,nocc,nocc,nocc), 'f8')
eris.ovoo = eris.feri1.create_dataset('ovoo', (nocc,nvir,nocc,nocc), 'f8', chunks=(nocc,1,nocc,nocc))
eris.ovov = eris.feri1.create_dataset('ovov', (nocc,nvir,nocc,nvir), 'f8', chunks=(nocc,1,nocc,nvir))
eris.ovvo = eris.feri1.create_dataset('ovvo', (nocc,nvir,nvir,nocc), 'f8', chunks=(nocc,1,nvir,nocc))
eris.ovvv = eris.feri1.create_dataset('ovvv', (nocc,nvir,nvir,nvir), 'f8')
eris.oovv = eris.feri1.create_dataset('oovv', (nocc,nocc,nvir,nvir), 'f8', chunks=(nocc,nocc,1,nvir))
eris.vvvv = eris.feri1.create_dataset('vvvv', (nvir,nvir,nvir,nvir), 'f8')
max_memory = max(MEMORYMIN, mycc.max_memory-lib.current_memory()[0])
ftmp = lib.H5TmpFile()
ao2mo.full(mol, mo_coeff, ftmp, max_memory=max_memory, verbose=log)
eri = ftmp['eri_mo']
nocc_pair = nocc*(nocc+1)//2
tril2sq = lib.square_mat_in_trilu_indices(nmo)
oo = eri[:nocc_pair]
eris.oooo[:] = ao2mo.restore(1, oo[:,:nocc_pair], nocc)
oovv = lib.take_2d(oo, tril2sq[:nocc,:nocc].ravel(), tril2sq[nocc:,nocc:].ravel())
eris.oovv[:] = oovv.reshape(nocc,nocc,nvir,nvir)
oo = oovv = None
tril2sq = lib.square_mat_in_trilu_indices(nmo)
blksize = min(nvir, max(BLKMIN, int(max_memory*1e6/8/nmo**3/2)))
for p0, p1 in lib.prange(0, nvir, blksize):
q0, q1 = p0+nocc, p1+nocc
off0 = q0*(q0+1)//2
off1 = q1*(q1+1)//2
buf = lib.unpack_tril(eri[off0:off1])
tmp = buf[ tril2sq[q0:q1,:nocc] - off0 ]
eris.ovoo[:,p0:p1] = tmp[:,:,:nocc,:nocc].transpose(1,0,2,3)
eris.ovvo[:,p0:p1] = tmp[:,:,nocc:,:nocc].transpose(1,0,2,3)
eris.ovov[:,p0:p1] = tmp[:,:,:nocc,nocc:].transpose(1,0,2,3)
eris.ovvv[:,p0:p1] = tmp[:,:,nocc:,nocc:].transpose(1,0,2,3)
tmp = buf[ tril2sq[q0:q1,nocc:q1] - off0 ]
eris.vvvv[p0:p1,:p1] = tmp[:,:,nocc:,nocc:]
if p0 > 0:
eris.vvvv[:p0,p0:p1] = tmp[:,:p0,nocc:,nocc:].transpose(1,0,2,3)
buf = tmp = None
log.timer('CCSD integral transformation', *cput0)
return eris
def _get_jk_2c_ints(mol, ia, ja):
zi = mol.atom_charge(ia)
zj = mol.atom_charge(ja)
ri = mol.atom_coord(ia) #?*lib.param.BOHR
rj = mol.atom_coord(ja) #?*lib.param.BOHR
w = numpy.zeros((10, 10))
e1b = numpy.zeros(10)
e2a = numpy.zeros(10)
enuc = numpy.zeros(1)
AM1_MODEL = 2
repp(zi, zj, ri, rj, w, e1b, e2a, enuc, MOPAC_ALP, MOPAC_DD, MOPAC_QQ,
MOPAC_AM, MOPAC_AD, MOPAC_AQ, MOPAC_IDEA_FN1, MOPAC_IDEA_FN2,
MOPAC_IDEA_FN3, AM1_MODEL)
tril2sq = lib.square_mat_in_trilu_indices(4)
w = w[:, tril2sq][tril2sq]
e1b = e1b[tril2sq]
e2a = e2a[tril2sq]
if mopac_param.CORE[zj] <= 1:
e2a = e2a[:1, :1]
w = w[:, :, :1, :1]
if mopac_param.CORE[zi] <= 1:
e1b = e1b[:1, :1]
w = w[:1, :1]
# enuc from repp integrals is wrong due to the unit of MOPAC_IDEA_FN2 and
# MOPAC_ALP
return w, e1b, e2a, enuc[0]
def get_jk(agf2, eri, rdm1, with_j=True, with_k=True):
''' Get the J/K matrices.
Args:
eri : ndarray or H5 dataset
Electronic repulsion integrals (NOT as _ChemistsERIs)
rdm1 : 2D array
Reduced density matrix
Kwargs:
with_j : bool
Whether to compute J. Default value is True
with_k : bool
Whether to compute K. Default value is True
Returns:
tuple of ndarrays corresponding to J and K, if either are
not requested then they are set to None.
'''
if isinstance(eri, np.ndarray):
vj, vk = _vhf.incore(eri, rdm1, with_j=with_j, with_k=with_k)
else:
nmo = rdm1.shape[0]
npair = nmo * (nmo + 1) // 2
vj = vk = None
if with_j:
rdm1_tril = lib.pack_tril(rdm1 + np.tril(rdm1, k=-1))
vj = np.zeros_like(rdm1_tril)
if with_k:
vk = np.zeros_like(rdm1)
blksize = _agf2.get_blksize(agf2.max_memory, (nmo * npair, nmo**3))
blksize = min(1, max(BLKMIN, blksize))
logger.debug1(agf2, 'blksize (ragf2.get_jk) = %d' % blksize)
tril2sq = lib.square_mat_in_trilu_indices(nmo)
for p0, p1 in lib.prange(0, nmo, blksize):
idx = list(np.concatenate(tril2sq[p0:p1]))
eri0 = eri[idx]
# vj built in tril layout with scaled rdm1_tril
if with_j:
vj[idx] = np.dot(eri0, rdm1_tril)
if with_k:
eri0 = lib.unpack_tril(eri0, axis=-1)
eri0 = eri0.reshape(p1 - p0, nmo, nmo, nmo)
vk[p0:p1] = lib.einsum('ijkl,jk->il', eri0, rdm1)
if with_j:
vj = lib.unpack_tril(vj)
return vj, vk
def _make_qmo_eris_outcore(agf2, eri, coeffs):
''' Returns H5 dataset
'''
cput0 = (logger.process_clock(), logger.perf_counter())
log = logger.Logger(agf2.stdout, agf2.verbose)
nmo = eri.nmo
ci, cj, ca = coeffs
ni = ci.shape[1]
nj = cj.shape[1]
na = ca.shape[1]
npair = nmo * (nmo + 1) // 2
mask = get_frozen_mask(agf2)
frozen = np.sum(~mask)
# possible to have incore MO, outcore QMO
if getattr(eri, 'feri', None) is None:
eri.feri = lib.H5TmpFile()
elif 'qmo' in eri.feri:
del eri.feri['qmo']
eri.feri.create_dataset('qmo', (nmo - frozen, ni, nj, na), 'f8')
blksize = _agf2.get_blksize(agf2.max_memory, (nmo * npair, nj * na, npair),
(nmo * ni, nj * na))
blksize = min(nmo, max(BLKMIN, blksize))
log.debug1('blksize (ragf2._make_qmo_eris_outcore) = %d', blksize)
tril2sq = lib.square_mat_in_trilu_indices(nmo)
q1 = 0
for p0, p1 in lib.prange(0, nmo, blksize):
if not np.any(mask[p0:p1]):
# block is fully frozen
continue
inds = np.arange(p0, p1)[mask[p0:p1]]
q0, q1 = q1, q1 + len(inds)
idx = list(np.concatenate(tril2sq[inds]))
buf = eri.eri[idx] # (blk, nmo, npair)
buf = buf.reshape((q1 - q0) * nmo, -1) # (blk*nmo, npair)
jasym, nja, cja, sja = ao2mo.incore._conc_mos(cj, ca, compact=True)
buf = ao2mo._ao2mo.nr_e2(buf, cja, sja, 's2kl', 's1')
buf = buf.reshape(q1 - q0, nmo, nj, na)
buf = lib.einsum('xpja,pi->xija', buf, ci)
eri.feri['qmo'][q0:q1] = np.asarray(buf, order='C')
log.timer('QMO integral transformation', *cput0)
return eri.feri['qmo']
def restore(symmetry, eri, norb, tao=None):
r'''Convert the 2e integrals (in Chemist's notation) between different
level of permutation symmetry (8-fold, 4-fold, or no symmetry)
Args:
symmetry : int or str
code to present the target symmetry of 2e integrals
| 's8' or '8' or 8 : 8-fold symmetry
| 's4' or '4' or 4 : 4-fold symmetry
| 's1' or '1' or 1 : no symmetry
| 's2ij' or '2ij' : symmetric ij pair for (ij|kl) (TODO)
| 's2ij' or '2kl' : symmetric kl pair for (ij|kl) (TODO)
Note the 4-fold symmetry requires (ij|kl) == (ij|lk) == (ij|lk)
while (ij|kl) != (kl|ij) is not required.
eri : ndarray
The symmetry of eri is determined by the size of eri and norb
norb : int
The symmetry of eri is determined by the size of eri and norb
Returns:
ndarray. The shape depends on the target symmetry.
| 8 : (norb*(norb+1)/2)*(norb*(norb+1)/2+1)/2
| 4 : (norb*(norb+1)/2, norb*(norb+1)/2)
| 1 : (norb, norb, norb, norb)
Examples:
>>> from pyscf import gto
>>> from pyscf.scf import _vhf
>>> from pyscf import ao2mo
>>> mol = gto.M(atom='O 0 0 0; H 0 1 0; H 0 0 1', basis='sto3g')
>>> eri = mol.intor('int2e')
>>> eri1 = ao2mo.restore(1, eri, mol.nao_nr())
>>> eri4 = ao2mo.restore(4, eri, mol.nao_nr())
>>> eri8 = ao2mo.restore(8, eri, mol.nao_nr())
>>> print(eri1.shape)
(7, 7, 7, 7)
>>> print(eri1.shape)
(28, 28)
>>> print(eri1.shape)
(406,)
'''
targetsym = _stand_sym_code(symmetry)
if targetsym not in ('8', '4', '1', '2kl', '2ij'):
raise ValueError('symmetry = %s' % symmetry)
if eri.dtype != numpy.double:
raise RuntimeError('Complex integrals not supported')
eri = numpy.asarray(eri, order='C')
npair = norb*(norb+1)//2
if eri.size == norb**4: # s1
if targetsym == '1':
return eri.reshape(norb,norb,norb,norb)
elif targetsym == '2kl':
eri = lib.pack_tril(eri.reshape(norb**2,norb,norb))
return eri.reshape(norb,norb,npair)
elif targetsym == '2ij':
eri = lib.pack_tril(eri.reshape(norb,norb,norb**2), axis=0)
return eri.reshape(npair,norb,norb)
else:
return _convert('1', targetsym, eri, norb)
elif eri.size == npair**2: # s4
if targetsym == '4':
return eri.reshape(npair,npair)
elif targetsym == '8':
return lib.pack_tril(eri.reshape(npair,npair))
elif targetsym == '2kl':
return lib.unpack_tril(eri, lib.SYMMETRIC, axis=0)
elif targetsym == '2ij':
return lib.unpack_tril(eri, lib.SYMMETRIC, axis=-1)
else:
return _convert('4', targetsym, eri, norb)
elif eri.size == npair*(npair+1)//2: # 8-fold
if targetsym == '8':
return eri.ravel()
elif targetsym == '4':
return lib.unpack_tril(eri.ravel(), lib.SYMMETRIC)
elif targetsym == '2kl':
return lib.unpack_tril(lib.unpack_tril(eri.ravel()), lib.SYMMETRIC, axis=0)
elif targetsym == '2ij':
return lib.unpack_tril(lib.unpack_tril(eri.ravel()), lib.SYMMETRIC, axis=-1)
else:
return _convert('8', targetsym, eri, norb)
elif eri.size == npair*norb**2 and eri.shape[0] == npair: # s2ij
if targetsym == '2ij':
return eri.reshape(npair,norb,norb)
elif targetsym == '8':
eri = lib.pack_tril(eri.reshape(npair,norb,norb))
return lib.pack_tril(eri)
elif targetsym == '4':
return lib.pack_tril(eri.reshape(npair,norb,norb))
elif targetsym == '1':
eri = lib.unpack_tril(eri.reshape(npair,norb**2), lib.SYMMETRIC, axis=0)
return eri.reshape(norb,norb,norb,norb)
elif targetsym == '2kl':
tril2sq = lib.square_mat_in_trilu_indices(norb)
trilidx = numpy.tril_indices(norb)
eri = lib.take_2d(eri.reshape(npair,norb**2), tril2sq.ravel(),
trilidx[0]*norb+trilidx[1])
return eri.reshape(norb,norb,npair)
elif eri.size == npair*norb**2 and eri.shape[-1] == npair: # s2kl
if targetsym == '2kl':
return eri.reshape(norb,norb,npair)
elif targetsym == '8':
eri = lib.pack_tril(eri.reshape(norb,norb,npair), axis=0)
return lib.pack_tril(eri)
elif targetsym == '4':
return lib.pack_tril(eri.reshape(norb,norb,npair), axis=0)
elif targetsym == '1':
eri = lib.unpack_tril(eri.reshape(norb**2,npair), lib.SYMMETRIC, axis=-1)
return eri.reshape(norb,norb,norb,norb)
elif targetsym == '2ij':
tril2sq = lib.square_mat_in_trilu_indices(norb)
trilidx = numpy.tril_indices(norb)
eri = lib.take_2d(eri.reshape(norb**2,npair),
trilidx[0]*norb+trilidx[1], tril2sq.ravel())
return eri.reshape(npair,norb,norb)
else:
raise RuntimeError('eri.size = %d, norb = %d' % (eri.size, norb))
def _make_eris_outcore(mycc, mo_coeff=None):
cput0 = (logger.process_clock(), logger.perf_counter())
log = logger.Logger(mycc.stdout, mycc.verbose)
eris = _PhysicistsERIs()
eris._common_init_(mycc, mo_coeff)
nocc = eris.nocc
nao, nmo = eris.mo_coeff.shape
nvir = nmo - nocc
assert(eris.mo_coeff.dtype == np.double)
mo_a = eris.mo_coeff[:nao//2]
mo_b = eris.mo_coeff[nao//2:]
orbspin = eris.orbspin
feri = eris.feri = lib.H5TmpFile()
dtype = np.result_type(eris.mo_coeff).char
eris.oooo = feri.create_dataset('oooo', (nocc,nocc,nocc,nocc), dtype)
eris.ooov = feri.create_dataset('ooov', (nocc,nocc,nocc,nvir), dtype)
eris.oovv = feri.create_dataset('oovv', (nocc,nocc,nvir,nvir), dtype)
eris.ovov = feri.create_dataset('ovov', (nocc,nvir,nocc,nvir), dtype)
eris.ovvo = feri.create_dataset('ovvo', (nocc,nvir,nvir,nocc), dtype)
eris.ovvv = feri.create_dataset('ovvv', (nocc,nvir,nvir,nvir), dtype)
if orbspin is None:
orbo_a = mo_a[:,:nocc]
orbv_a = mo_a[:,nocc:]
orbo_b = mo_b[:,:nocc]
orbv_b = mo_b[:,nocc:]
max_memory = mycc.max_memory-lib.current_memory()[0]
blksize = min(nocc, max(2, int(max_memory*1e6/8/(nmo**3*2))))
max_memory = max(MEMORYMIN, max_memory)
fswap = lib.H5TmpFile()
ao2mo.kernel(mycc.mol, (orbo_a,mo_a,mo_a,mo_a), fswap, 'aaaa',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbo_a,mo_a,mo_b,mo_b), fswap, 'aabb',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbo_b,mo_b,mo_a,mo_a), fswap, 'bbaa',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbo_b,mo_b,mo_b,mo_b), fswap, 'bbbb',
max_memory=max_memory, verbose=log)
for p0, p1 in lib.prange(0, nocc, blksize):
tmp = np.asarray(fswap['aaaa'][p0*nmo:p1*nmo])
tmp += np.asarray(fswap['aabb'][p0*nmo:p1*nmo])
tmp += np.asarray(fswap['bbaa'][p0*nmo:p1*nmo])
tmp += np.asarray(fswap['bbbb'][p0*nmo:p1*nmo])
tmp = lib.unpack_tril(tmp).reshape(p1-p0,nmo,nmo,nmo)
eris.oooo[p0:p1] = (tmp[:,:nocc,:nocc,:nocc].transpose(0,2,1,3) -
tmp[:,:nocc,:nocc,:nocc].transpose(0,2,3,1))
eris.ooov[p0:p1] = (tmp[:,:nocc,:nocc,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,:nocc,:nocc].transpose(0,2,3,1))
eris.ovvv[p0:p1] = (tmp[:,nocc:,nocc:,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,nocc:,nocc:].transpose(0,2,3,1))
eris.oovv[p0:p1] = (tmp[:,nocc:,:nocc,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,:nocc,nocc:].transpose(0,2,3,1))
eris.ovov[p0:p1] = (tmp[:,:nocc,nocc:,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,nocc:,:nocc].transpose(0,2,3,1))
eris.ovvo[p0:p1] = (tmp[:,nocc:,nocc:,:nocc].transpose(0,2,1,3) -
tmp[:,:nocc,nocc:,nocc:].transpose(0,2,3,1))
tmp = None
cput0 = log.timer_debug1('transforming ovvv', *cput0)
eris.vvvv = feri.create_dataset('vvvv', (nvir,nvir,nvir,nvir), dtype)
tril2sq = lib.square_mat_in_trilu_indices(nvir)
fswap = lib.H5TmpFile()
ao2mo.kernel(mycc.mol, (orbv_a,orbv_a,orbv_a,orbv_a), fswap, 'aaaa',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbv_a,orbv_a,orbv_b,orbv_b), fswap, 'aabb',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbv_b,orbv_b,orbv_a,orbv_a), fswap, 'bbaa',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbv_b,orbv_b,orbv_b,orbv_b), fswap, 'bbbb',
max_memory=max_memory, verbose=log)
for p0, p1 in lib.prange(0, nvir, blksize):
off0 = p0*(p0+1)//2
off1 = p1*(p1+1)//2
tmp = np.asarray(fswap['aaaa'][off0:off1])
tmp += np.asarray(fswap['aabb'][off0:off1])
tmp += np.asarray(fswap['bbaa'][off0:off1])
tmp += np.asarray(fswap['bbbb'][off0:off1])
if p0 > 0:
c = tmp[ tril2sq[p0:p1,:p0] - off0 ]
c = lib.unpack_tril(c.reshape((p1-p0)*p0,-1))
eris.vvvv[p0:p1,:p0] = c.reshape(p1-p0,p0,nvir,nvir)
c = tmp[ tril2sq[:p1,p0:p1] - off0 ]
c = lib.unpack_tril(c.reshape((p1-p0)*p1,-1))
eris.vvvv[:p1,p0:p1] = c.reshape(p1,p1-p0,nvir,nvir)
tmp = None
for p0, p1 in lib.prange(0, nvir, blksize):
tmp = np.asarray(eris.vvvv[p0:p1])
eris.vvvv[p0:p1] = tmp.transpose(0,2,1,3) - tmp.transpose(0,2,3,1)
cput0 = log.timer_debug1('transforming vvvv', *cput0)
else: # with orbspin
mo = mo_a + mo_b
orbo = mo[:,:nocc]
orbv = mo[:,nocc:]
max_memory = mycc.max_memory-lib.current_memory()[0]
blksize = min(nocc, max(2, int(max_memory*1e6/8/(nmo**3*2))))
max_memory = max(MEMORYMIN, max_memory)
fswap = lib.H5TmpFile()
ao2mo.kernel(mycc.mol, (orbo,mo,mo,mo), fswap,
max_memory=max_memory, verbose=log)
sym_forbid = orbspin[:,None] != orbspin
for p0, p1 in lib.prange(0, nocc, blksize):
tmp = np.asarray(fswap['eri_mo'][p0*nmo:p1*nmo])
tmp = lib.unpack_tril(tmp).reshape(p1-p0,nmo,nmo,nmo)
tmp[sym_forbid[p0:p1]] = 0
tmp[:,:,sym_forbid] = 0
eris.oooo[p0:p1] = (tmp[:,:nocc,:nocc,:nocc].transpose(0,2,1,3) -
tmp[:,:nocc,:nocc,:nocc].transpose(0,2,3,1))
eris.ooov[p0:p1] = (tmp[:,:nocc,:nocc,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,:nocc,:nocc].transpose(0,2,3,1))
eris.ovvv[p0:p1] = (tmp[:,nocc:,nocc:,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,nocc:,nocc:].transpose(0,2,3,1))
eris.oovv[p0:p1] = (tmp[:,nocc:,:nocc,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,:nocc,nocc:].transpose(0,2,3,1))
eris.ovov[p0:p1] = (tmp[:,:nocc,nocc:,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,nocc:,:nocc].transpose(0,2,3,1))
eris.ovvo[p0:p1] = (tmp[:,nocc:,nocc:,:nocc].transpose(0,2,1,3) -
tmp[:,:nocc,nocc:,nocc:].transpose(0,2,3,1))
tmp = None
cput0 = log.timer_debug1('transforming ovvv', *cput0)
eris.vvvv = feri.create_dataset('vvvv', (nvir,nvir,nvir,nvir), dtype)
sym_forbid = (orbspin[nocc:,None]!=orbspin[nocc:])[np.tril_indices(nvir)]
tril2sq = lib.square_mat_in_trilu_indices(nvir)
fswap = lib.H5TmpFile()
ao2mo.kernel(mycc.mol, orbv, fswap, max_memory=max_memory, verbose=log)
for p0, p1 in lib.prange(0, nvir, blksize):
off0 = p0*(p0+1)//2
off1 = p1*(p1+1)//2
tmp = np.asarray(fswap['eri_mo'][off0:off1])
tmp[sym_forbid[off0:off1]] = 0
tmp[:,sym_forbid] = 0
if p0 > 0:
c = tmp[ tril2sq[p0:p1,:p0] - off0 ]
c = lib.unpack_tril(c.reshape((p1-p0)*p0,-1))
eris.vvvv[p0:p1,:p0] = c.reshape(p1-p0,p0,nvir,nvir)
c = tmp[ tril2sq[:p1,p0:p1] - off0 ]
c = lib.unpack_tril(c.reshape((p1-p0)*p1,-1))
eris.vvvv[:p1,p0:p1] = c.reshape(p1,p1-p0,nvir,nvir)
tmp = None
for p0, p1 in lib.prange(0, nvir, blksize):
tmp = np.asarray(eris.vvvv[p0:p1])
eris.vvvv[p0:p1] = tmp.transpose(0,2,1,3) - tmp.transpose(0,2,3,1)
cput0 = log.timer_debug1('transforming vvvv', *cput0)
return eris
def _make_qmo_eris_outcore(agf2, eri, coeffs_a, coeffs_b, spin=None):
''' Returns nested tuple of H5 dataset
spin = None: ((aaaa, aabb), (bbaa, bbbb))
spin = 0: (aaaa, aabb)
spin = 1: (bbbb, bbaa)
'''
cput0 = (time.clock(), time.time())
log = logger.Logger(agf2.stdout, agf2.verbose)
nmo = eri.nmo
nmoa, nmob = nmo
cxa = np.eye(nmoa)
cxb = np.eye(nmob)
mask = get_frozen_mask(agf2)
frozena = np.sum(~mask[0])
frozenb = np.sum(~mask[1])
npaira, npairb = nmoa*(nmoa+1)//2, nmob*(nmob+1)//2
cia, cja, caa = coeffs_a
cib, cjb, cab = coeffs_b
nia, nja, naa = [x.shape[1] for x in coeffs_a]
nib, njb, nab = [x.shape[1] for x in coeffs_b]
# possible to have incore MO, outcore QMO
if getattr(eri, 'feri', None) is None:
eri.feri = lib.H5TmpFile()
else:
for key in ['aa', 'ab', 'ba', 'bb']:
if 'qmo/%s'%key in eri.feri:
del eri.feri['qmo/%s'%key]
if spin is None or spin == 0:
eri.feri.create_dataset('qmo/aa', (nmoa-frozena, nia, nja, naa), 'f8')
eri.feri.create_dataset('qmo/ab', (nmoa-frozena, nia, njb, nab), 'f8')
blksize = _agf2.get_blksize(agf2.max_memory, (nmoa**3, nmoa*nja*naa),
(nmoa*nmob**2, nmoa*njb*nab))
blksize = min(nmoa, max(BLKMIN, blksize))
log.debug1('blksize (uagf2._make_qmo_eris_outcore) = %d', blksize)
tril2sq = lib.square_mat_in_trilu_indices(nmoa)
q1 = 0
for p0, p1 in lib.prange(0, nmoa, blksize):
if not np.any(mask[0][p0:p1]):
# block is fully frozen
continue
inds = np.arange(p0, p1)[mask[0][p0:p1]]
q0, q1 = q1, q1 + len(inds)
idx = list(np.concatenate(tril2sq[inds]))
# aa
buf = eri.eri_aa[idx] # (blk, nmoa, npaira)
buf = buf.reshape((q1-q0)*nmoa, -1) # (blk*nmoa, npaira)
jasym_aa, nja_aa, cja_aa, sja_aa = ao2mo.incore._conc_mos(cja, caa)
buf = ao2mo._ao2mo.nr_e2(buf, cja_aa, sja_aa, 's2kl', 's1')
buf = buf.reshape(q1-q0, nmoa, nja, naa)
buf = lib.einsum('xpja,pi->xija', buf, cia)
eri.feri['qmo/aa'][q0:q1] = np.asarray(buf, order='C')
# ab
buf = eri.eri_ab[idx] # (blk, nmoa, npairb)
buf = buf.reshape((q1-q0)*nmob, -1) # (blk*nmoa, npairb)
jasym_ab, nja_ab, cja_ab, sja_ab = ao2mo.incore._conc_mos(cjb, cab)
buf = ao2mo._ao2mo.nr_e2(buf, cja_ab, sja_ab, 's2kl', 's1')
buf = buf.reshape(q1-q0, nmoa, njb, nab)
buf = lib.einsum('xpja,pi->xija', buf, cia)
eri.feri['qmo/ab'][q0:q1] = np.asarray(buf, order='C')
if spin is None or spin == 1:
eri.feri.create_dataset('qmo/ba', (nmob-frozenb, nib, nja, naa), 'f8')
eri.feri.create_dataset('qmo/bb', (nmob-frozenb, nib, njb, nab), 'f8')
max_memory = agf2.max_memory - lib.current_memory()[0]
blksize = int((max_memory/8e-6) / max(nmob**3+nmob*njb*nab,
nmob*nmoa**2*nja*naa))
blksize = min(nmob, max(BLKMIN, blksize))
log.debug1('blksize (uagf2._make_qmo_eris_outcore) = %d', blksize)
tril2sq = lib.square_mat_in_trilu_indices(nmob)
q1 = 0
for p0, p1 in lib.prange(0, nmob, blksize):
if not np.any(mask[1][p0:p1]):
# block is fully frozen
continue
inds = np.arange(p0, p1)[mask[1][p0:p1]]
q0, q1 = q1, q1 + len(inds)
idx = list(np.concatenate(tril2sq[inds]))
# ba
buf = eri.eri_ba[idx] # (blk, nmob, npaira)
buf = buf.reshape((q1-q0)*nmob, -1) # (blk*nmob, npaira)
jasym_ba, nja_ba, cja_ba, sja_ba = ao2mo.incore._conc_mos(cja, caa)
buf = ao2mo._ao2mo.nr_e2(buf, cja_ba, sja_ba, 's2kl', 's1')
buf = buf.reshape(q1-q0, nmob, nja, naa)
buf = lib.einsum('xpja,pi->xija', buf, cib)
eri.feri['qmo/ba'][q0:q1] = np.asarray(buf, order='C')
# bb
buf = eri.eri_bb[idx] # (blk, nmob, npairb)
buf = buf.reshape((q1-q0)*nmob, -1) # (blk*nmob, npairb)
jasym_bb, nja_bb, cja_bb, sja_bb = ao2mo.incore._conc_mos(cjb, cab)
buf = ao2mo._ao2mo.nr_e2(buf, cja_bb, sja_bb, 's2kl', 's1')
buf = buf.reshape(q1-q0, nmob, njb, nab)
buf = lib.einsum('xpja,pi->xija', buf, cib)
eri.feri['qmo/bb'][q0:q1] = np.asarray(buf, order='C')
if spin is None:
qeri = ((eri.feri['qmo/aa'], eri.feri['qmo/ab']),
(eri.feri['qmo/ba'], eri.feri['qmo/bb']))
elif spin == 0:
qeri = (eri.feri['qmo/aa'], eri.feri['qmo/ab'])
elif spin == 1:
qeri = (eri.feri['qmo/bb'], eri.feri['qmo/ba'])
log.timer('QMO integral transformation', *cput0)
return qeri
def _contract_vvvv_t2(mycc, mol, vvL, t2, out=None, verbose=None):
'''Ht2 = numpy.einsum('ijcd,acdb->ijab', t2, vvvv)
Args:
vvvv : None or integral object
if vvvv is None, contract t2 to AO-integrals using AO-direct algorithm
'''
_dgemm = lib.numpy_helper._dgemm
time0 = time.clock(), time.time()
log = logger.new_logger(mol, verbose)
naux = vvL.shape[-1]
nvira, nvirb = t2.shape[-2:]
x2 = t2.reshape(-1, nvira, nvirb)
nocc2 = x2.shape[0]
nvir2 = nvira * nvirb
Ht2 = numpy.ndarray(x2.shape, buffer=out)
Ht2[:] = 0
max_memory = max(MEMORYMIN, mycc.max_memory - lib.current_memory()[0])
def contract_blk_(eri, i0, i1, j0, j1):
ic = i1 - i0
jc = j1 - j0
#:Ht2[:,j0:j1] += numpy.einsum('xef,efab->xab', x2[:,i0:i1], eri)
_dgemm('N', 'N', nocc2, jc * nvirb, ic * nvirb, x2.reshape(-1, nvir2),
eri.reshape(-1, jc * nvirb), Ht2.reshape(-1, nvir2), 1, 1,
i0 * nvirb, 0, j0 * nvirb)
if i0 > j0:
#:Ht2[:,i0:i1] += numpy.einsum('xef,abef->xab', x2[:,j0:j1], eri)
_dgemm('N', 'T', nocc2, ic * nvirb, jc * nvirb,
x2.reshape(-1, nvir2), eri.reshape(-1, jc * nvirb),
Ht2.reshape(-1, nvir2), 1, 1, j0 * nvirb, 0, i0 * nvirb)
#TODO: check if vvL can be entirely loaded into memory
nvir_pair = nvirb * (nvirb + 1) // 2
dmax = numpy.sqrt(max_memory * .7e6 / 8 / nvirb**2 / 2)
dmax = int(min((nvira + 3) // 4, max(ccsd.BLKMIN, dmax)))
vvblk = (max_memory * 1e6 / 8 - dmax**2 * (nvirb**2 * 1.5 + naux)) / naux
vvblk = int(min((nvira + 3) // 4, max(ccsd.BLKMIN, vvblk / naux)))
eribuf = numpy.empty((dmax, dmax, nvir_pair))
loadbuf = numpy.empty((dmax, dmax, nvirb, nvirb))
tril2sq = lib.square_mat_in_trilu_indices(nvira)
for i0, i1 in lib.prange(0, nvira, dmax):
off0 = i0 * (i0 + 1) // 2
off1 = i1 * (i1 + 1) // 2
vvL0 = _cp(vvL[off0:off1])
for j0, j1 in lib.prange(0, i1, dmax):
ijL = vvL0[tril2sq[i0:i1, j0:j1] - off0].reshape(-1, naux)
eri = numpy.ndarray(((i1 - i0) * (j1 - j0), nvir_pair),
buffer=eribuf)
for p0, p1 in lib.prange(0, nvir_pair, vvblk):
vvL1 = _cp(vvL[p0:p1])
eri[:, p0:p1] = lib.ddot(ijL, vvL1.T)
vvL1 = None
tmp = numpy.ndarray((i1 - i0, nvirb, j1 - j0, nvirb),
buffer=loadbuf)
_ccsd.libcc.CCload_eri(tmp.ctypes.data_as(ctypes.c_void_p),
eri.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int * 4)(i0, i1, j0, j1),
ctypes.c_int(nvirb))
contract_blk_(tmp, i0, i1, j0, j1)
time0 = log.timer_debug1('vvvv [%d:%d,%d:%d]' % (i0, i1, j0, j1),
*time0)
return Ht2.reshape(t2.shape)
def _add_ovvv_(mycc, t1, t2, eris, fvv, t1new, t2new, fswap):
time1 = logger.process_clock(), logger.perf_counter()
log = logger.Logger(mycc.stdout, mycc.verbose)
nocc, nvir = t1.shape
nvir_pair = nvir * (nvir + 1) // 2
if fswap is None:
wVOov = numpy.zeros((nvir, nocc, nocc, nvir))
else:
wVOov = fswap.create_dataset('wVOov', (nvir, nocc, nocc, nvir), 'f8')
wooVV = numpy.zeros((nocc, nocc * nvir_pair))
max_memory = mycc.max_memory - lib.current_memory()[0]
unit = nocc * nvir**2 * 3 + nocc**2 * nvir + 2
blksize = min(
nvir, max(BLKMIN, int((max_memory * .95e6 / 8 - wooVV.size) / unit)))
if not mycc.direct:
unit = nocc * nvir**2 * 3 + nocc**2 * nvir + 2 + nocc * nvir**2 + nocc * nvir
blksize = min(
nvir,
max(
BLKMIN,
int((max_memory * .95e6 / 8 - wooVV.size - nocc**2 * nvir) /
unit)))
log.debug1('max_memory %d MB, nocc,nvir = %d,%d blksize = %d',
max_memory, nocc, nvir, blksize)
def load_ovvv(buf, p0):
if p0 < nvir:
p1 = min(nvir, p0 + blksize)
buf[:p1 - p0] = eris.ovvv[:, p0:p1].transpose(1, 0, 2)
with lib.call_in_background(load_ovvv, sync=not mycc.async_io) as prefetch:
buf = numpy.empty((blksize, nocc, nvir_pair))
buf_prefetch = numpy.empty((blksize, nocc, nvir_pair))
load_ovvv(buf_prefetch, 0)
for p0, p1 in lib.prange(0, nvir, blksize):
buf, buf_prefetch = buf_prefetch, buf
prefetch(buf_prefetch, p1)
eris_vovv = buf[:p1 - p0]
eris_vovv = lib.unpack_tril(
eris_vovv.reshape((p1 - p0) * nocc, nvir_pair))
eris_vovv = eris_vovv.reshape(p1 - p0, nocc, nvir, nvir)
wVOov[p0:p1] = lib.einsum('biac,jc->bija', eris_vovv, t1)
theta = t2[:, :, p0:p1].transpose(1, 2, 0, 3) * 2
theta -= t2[:, :, p0:p1].transpose(0, 2, 1, 3)
t1new += lib.einsum('icjb,cjba->ia', theta, eris_vovv)
theta = None
time1 = log.timer_debug1('vovv [%d:%d]' % (p0, p1), *time1)
if fswap is None:
wooVV = lib.unpack_tril(wooVV.reshape(nocc**2, nvir_pair))
return wVOov, wooVV.reshape(nocc, nocc, nvir,
nvir).transpose(2, 1, 0, 3)
else:
fswap.create_dataset('wVooV', (nvir, nocc, nocc, nvir), 'f8')
wooVV = wooVV.reshape(nocc, nocc, nvir_pair)
tril2sq = lib.square_mat_in_trilu_indices(nvir)
for p0, p1 in lib.prange(0, nvir, blksize):
fswap['wVooV'][p0:p1] = wooVV[:, :, tril2sq[p0:p1]].transpose(
2, 1, 0, 3)
return fswap['wVOov'], fswap['wVooV']
def _contract_vvvv_t2(mycc, mol, vvL, t2, out=None, verbose=None):
'''Ht2 = numpy.einsum('ijcd,acdb->ijab', t2, vvvv)
Args:
vvvv : None or integral object
if vvvv is None, contract t2 to AO-integrals using AO-direct algorithm
'''
_dgemm = lib.numpy_helper._dgemm
time0 = time.clock(), time.time()
log = logger.new_logger(mol, verbose)
naux = vvL.shape[-1]
nvira, nvirb = t2.shape[-2:]
x2 = t2.reshape(-1,nvira,nvirb)
nocc2 = x2.shape[0]
nvir2 = nvira * nvirb
Ht2 = numpy.ndarray(x2.shape, buffer=out)
Ht2[:] = 0
max_memory = max(MEMORYMIN, mycc.max_memory - lib.current_memory()[0])
def contract_blk_(eri, i0, i1, j0, j1):
ic = i1 - i0
jc = j1 - j0
#:Ht2[:,j0:j1] += numpy.einsum('xef,efab->xab', x2[:,i0:i1], eri)
_dgemm('N', 'N', nocc2, jc*nvirb, ic*nvirb,
x2.reshape(-1,nvir2), eri.reshape(-1,jc*nvirb),
Ht2.reshape(-1,nvir2), 1, 1, i0*nvirb, 0, j0*nvirb)
if i0 > j0:
#:Ht2[:,i0:i1] += numpy.einsum('xef,abef->xab', x2[:,j0:j1], eri)
_dgemm('N', 'T', nocc2, ic*nvirb, jc*nvirb,
x2.reshape(-1,nvir2), eri.reshape(-1,jc*nvirb),
Ht2.reshape(-1,nvir2), 1, 1, j0*nvirb, 0, i0*nvirb)
#TODO: check if vvL can be entirely loaded into memory
nvir_pair = nvirb * (nvirb+1) // 2
dmax = numpy.sqrt(max_memory*.7e6/8/nvirb**2/2)
dmax = int(min((nvira+3)//4, max(ccsd.BLKMIN, dmax)))
vvblk = (max_memory*1e6/8 - dmax**2*(nvirb**2*1.5+naux))/naux
vvblk = int(min((nvira+3)//4, max(ccsd.BLKMIN, vvblk/naux)))
eribuf = numpy.empty((dmax,dmax,nvir_pair))
loadbuf = numpy.empty((dmax,dmax,nvirb,nvirb))
tril2sq = lib.square_mat_in_trilu_indices(nvira)
for i0, i1 in lib.prange(0, nvira, dmax):
off0 = i0*(i0+1)//2
off1 = i1*(i1+1)//2
vvL0 = _cp(vvL[off0:off1])
for j0, j1 in lib.prange(0, i1, dmax):
ijL = vvL0[tril2sq[i0:i1,j0:j1] - off0].reshape(-1,naux)
eri = numpy.ndarray(((i1-i0)*(j1-j0),nvir_pair), buffer=eribuf)
for p0, p1 in lib.prange(0, nvir_pair, vvblk):
vvL1 = _cp(vvL[p0:p1])
eri[:,p0:p1] = lib.ddot(ijL, vvL1.T)
vvL1 = None
tmp = numpy.ndarray((i1-i0,nvirb,j1-j0,nvirb), buffer=loadbuf)
_ccsd.libcc.CCload_eri(tmp.ctypes.data_as(ctypes.c_void_p),
eri.ctypes.data_as(ctypes.c_void_p),
(ctypes.c_int*4)(i0, i1, j0, j1),
ctypes.c_int(nvirb))
contract_blk_(tmp, i0, i1, j0, j1)
time0 = log.timer_debug1('vvvv [%d:%d,%d:%d]'%(i0,i1,j0,j1), *time0)
return Ht2.reshape(t2.shape)
def restore(symmetry, eri, norb, tao=None):
r'''Convert the 2e integrals (in Chemist's notation) between different
level of permutation symmetry (8-fold, 4-fold, or no symmetry)
Args:
symmetry : int or str
code to present the target symmetry of 2e integrals
| 's8' or '8' or 8 : 8-fold symmetry
| 's4' or '4' or 4 : 4-fold symmetry
| 's1' or '1' or 1 : no symmetry
| 's2ij' or '2ij' : symmetric ij pair for (ij|kl) (TODO)
| 's2ij' or '2kl' : symmetric kl pair for (ij|kl) (TODO)
Note the 4-fold symmetry requires (ij|kl) == (ij|lk) == (ij|lk)
while (ij|kl) != (kl|ij) is not required.
eri : ndarray
The symmetry of eri is determined by the size of eri and norb
norb : int
The symmetry of eri is determined by the size of eri and norb
Returns:
ndarray. The shape depends on the target symmetry.
| 8 : (norb*(norb+1)/2)*(norb*(norb+1)/2+1)/2
| 4 : (norb*(norb+1)/2, norb*(norb+1)/2)
| 1 : (norb, norb, norb, norb)
Examples:
>>> from pyscf import gto
>>> from pyscf.scf import _vhf
>>> from pyscf import ao2mo
>>> mol = gto.M(atom='O 0 0 0; H 0 1 0; H 0 0 1', basis='sto3g')
>>> eri = mol.intor('int2e')
>>> eri1 = ao2mo.restore(1, eri, mol.nao_nr())
>>> eri4 = ao2mo.restore(4, eri, mol.nao_nr())
>>> eri8 = ao2mo.restore(8, eri, mol.nao_nr())
>>> print(eri1.shape)
(7, 7, 7, 7)
>>> print(eri1.shape)
(28, 28)
>>> print(eri1.shape)
(406,)
'''
targetsym = _stand_sym_code(symmetry)
if targetsym not in ('8', '4', '1', '2kl', '2ij'):
raise ValueError('symmetry = %s' % symmetry)
if eri.dtype != numpy.double:
raise RuntimeError('Complex integrals not supported')
eri = numpy.asarray(eri, order='C')
npair = norb * (norb + 1) // 2
if eri.size == norb**4: # s1
if targetsym == '1':
return eri.reshape(norb, norb, norb, norb)
elif targetsym == '2kl':
eri = lib.pack_tril(eri.reshape(norb**2, norb, norb))
return eri.reshape(norb, norb, npair)
elif targetsym == '2ij':
eri = lib.pack_tril(eri.reshape(norb, norb, norb**2), axis=0)
return eri.reshape(npair, norb, norb)
else:
return _convert('1', targetsym, eri, norb)
elif eri.size == npair**2: # s4
if targetsym == '4':
return eri.reshape(npair, npair)
elif targetsym == '8':
return lib.pack_tril(eri.reshape(npair, npair))
elif targetsym == '2kl':
return lib.unpack_tril(eri, lib.SYMMETRIC, axis=0)
elif targetsym == '2ij':
return lib.unpack_tril(eri, lib.SYMMETRIC, axis=-1)
else:
return _convert('4', targetsym, eri, norb)
elif eri.size == npair * (npair + 1) // 2: # 8-fold
if targetsym == '8':
return eri.ravel()
elif targetsym == '4':
return lib.unpack_tril(eri.ravel(), lib.SYMMETRIC)
elif targetsym == '2kl':
return lib.unpack_tril(lib.unpack_tril(eri.ravel()),
lib.SYMMETRIC,
axis=0)
elif targetsym == '2ij':
return lib.unpack_tril(lib.unpack_tril(eri.ravel()),
lib.SYMMETRIC,
axis=-1)
else:
return _convert('8', targetsym, eri, norb)
elif eri.size == npair * norb**2 and eri.shape[0] == npair: # s2ij
if targetsym == '2ij':
return eri.reshape(npair, norb, norb)
elif targetsym == '8':
eri = lib.pack_tril(eri.reshape(npair, norb, norb))
return lib.pack_tril(eri)
elif targetsym == '4':
return lib.pack_tril(eri.reshape(npair, norb, norb))
elif targetsym == '1':
eri = lib.unpack_tril(eri.reshape(npair, norb**2),
lib.SYMMETRIC,
axis=0)
return eri.reshape(norb, norb, norb, norb)
elif targetsym == '2kl':
tril2sq = lib.square_mat_in_trilu_indices(norb)
trilidx = numpy.tril_indices(norb)
eri = lib.take_2d(eri.reshape(npair, norb**2), tril2sq.ravel(),
trilidx[0] * norb + trilidx[1])
return eri.reshape(norb, norb, npair)
elif eri.size == npair * norb**2 and eri.shape[-1] == npair: # s2kl
if targetsym == '2kl':
return eri.reshape(norb, norb, npair)
elif targetsym == '8':
eri = lib.pack_tril(eri.reshape(norb, norb, npair), axis=0)
return lib.pack_tril(eri)
elif targetsym == '4':
return lib.pack_tril(eri.reshape(norb, norb, npair), axis=0)
elif targetsym == '1':
eri = lib.unpack_tril(eri.reshape(norb**2, npair),
lib.SYMMETRIC,
axis=-1)
return eri.reshape(norb, norb, norb, norb)
elif targetsym == '2ij':
tril2sq = lib.square_mat_in_trilu_indices(norb)
trilidx = numpy.tril_indices(norb)
eri = lib.take_2d(eri.reshape(norb**2, npair),
trilidx[0] * norb + trilidx[1], tril2sq.ravel())
return eri.reshape(npair, norb, norb)
else:
raise RuntimeError('eri.size = %d, norb = %d' % (eri.size, norb))
def _make_eris_outcore(mycc, mo_coeff=None):
cput0 = (time.clock(), time.time())
log = logger.Logger(mycc.stdout, mycc.verbose)
eris = _PhysicistsERIs()
eris._common_init_(mycc, mo_coeff)
nocc = eris.nocc
nao, nmo = eris.mo_coeff.shape
nvir = nmo - nocc
assert(eris.mo_coeff.dtype == np.double)
mo_a = eris.mo_coeff[:nao//2]
mo_b = eris.mo_coeff[nao//2:]
orbspin = eris.orbspin
feri = eris.feri = lib.H5TmpFile()
dtype = np.result_type(eris.mo_coeff).char
eris.oooo = feri.create_dataset('oooo', (nocc,nocc,nocc,nocc), dtype)
eris.ooov = feri.create_dataset('ooov', (nocc,nocc,nocc,nvir), dtype)
eris.oovv = feri.create_dataset('oovv', (nocc,nocc,nvir,nvir), dtype)
eris.ovov = feri.create_dataset('ovov', (nocc,nvir,nocc,nvir), dtype)
eris.ovvo = feri.create_dataset('ovvo', (nocc,nvir,nvir,nocc), dtype)
eris.ovvv = feri.create_dataset('ovvv', (nocc,nvir,nvir,nvir), dtype)
if orbspin is None:
orbo_a = mo_a[:,:nocc]
orbv_a = mo_a[:,nocc:]
orbo_b = mo_b[:,:nocc]
orbv_b = mo_b[:,nocc:]
max_memory = mycc.max_memory-lib.current_memory()[0]
blksize = min(nocc, max(2, int(max_memory*1e6/8/(nmo**3*2))))
max_memory = max(MEMORYMIN, max_memory)
fswap = lib.H5TmpFile()
ao2mo.kernel(mycc.mol, (orbo_a,mo_a,mo_a,mo_a), fswap, 'aaaa',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbo_a,mo_a,mo_b,mo_b), fswap, 'aabb',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbo_b,mo_b,mo_a,mo_a), fswap, 'bbaa',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbo_b,mo_b,mo_b,mo_b), fswap, 'bbbb',
max_memory=max_memory, verbose=log)
for p0, p1 in lib.prange(0, nocc, blksize):
tmp = np.asarray(fswap['aaaa'][p0*nmo:p1*nmo])
tmp += np.asarray(fswap['aabb'][p0*nmo:p1*nmo])
tmp += np.asarray(fswap['bbaa'][p0*nmo:p1*nmo])
tmp += np.asarray(fswap['bbbb'][p0*nmo:p1*nmo])
tmp = lib.unpack_tril(tmp).reshape(p1-p0,nmo,nmo,nmo)
eris.oooo[p0:p1] = (tmp[:,:nocc,:nocc,:nocc].transpose(0,2,1,3) -
tmp[:,:nocc,:nocc,:nocc].transpose(0,2,3,1))
eris.ooov[p0:p1] = (tmp[:,:nocc,:nocc,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,:nocc,:nocc].transpose(0,2,3,1))
eris.ovvv[p0:p1] = (tmp[:,nocc:,nocc:,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,nocc:,nocc:].transpose(0,2,3,1))
eris.oovv[p0:p1] = (tmp[:,nocc:,:nocc,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,:nocc,nocc:].transpose(0,2,3,1))
eris.ovov[p0:p1] = (tmp[:,:nocc,nocc:,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,nocc:,:nocc].transpose(0,2,3,1))
eris.ovvo[p0:p1] = (tmp[:,nocc:,nocc:,:nocc].transpose(0,2,1,3) -
tmp[:,:nocc,nocc:,nocc:].transpose(0,2,3,1))
tmp = None
cput0 = log.timer_debug1('transforming ovvv', *cput0)
eris.vvvv = feri.create_dataset('vvvv', (nvir,nvir,nvir,nvir), dtype)
tril2sq = lib.square_mat_in_trilu_indices(nvir)
fswap = lib.H5TmpFile()
ao2mo.kernel(mycc.mol, (orbv_a,orbv_a,orbv_a,orbv_a), fswap, 'aaaa',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbv_a,orbv_a,orbv_b,orbv_b), fswap, 'aabb',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbv_b,orbv_b,orbv_a,orbv_a), fswap, 'bbaa',
max_memory=max_memory, verbose=log)
ao2mo.kernel(mycc.mol, (orbv_b,orbv_b,orbv_b,orbv_b), fswap, 'bbbb',
max_memory=max_memory, verbose=log)
for p0, p1 in lib.prange(0, nvir, blksize):
off0 = p0*(p0+1)//2
off1 = p1*(p1+1)//2
tmp = np.asarray(fswap['aaaa'][off0:off1])
tmp += np.asarray(fswap['aabb'][off0:off1])
tmp += np.asarray(fswap['bbaa'][off0:off1])
tmp += np.asarray(fswap['bbbb'][off0:off1])
if p0 > 0:
c = tmp[ tril2sq[p0:p1,:p0] - off0 ]
c = lib.unpack_tril(c.reshape((p1-p0)*p0,-1))
eris.vvvv[p0:p1,:p0] = c.reshape(p1-p0,p0,nvir,nvir)
c = tmp[ tril2sq[:p1,p0:p1] - off0 ]
c = lib.unpack_tril(c.reshape((p1-p0)*p1,-1))
eris.vvvv[:p1,p0:p1] = c.reshape(p1,p1-p0,nvir,nvir)
tmp = None
for p0, p1 in lib.prange(0, nvir, blksize):
tmp = np.asarray(eris.vvvv[p0:p1])
eris.vvvv[p0:p1] = tmp.transpose(0,2,1,3) - tmp.transpose(0,2,3,1)
cput0 = log.timer_debug1('transforming vvvv', *cput0)
else: # with orbspin
mo = mo_a + mo_b
orbo = mo[:,:nocc]
orbv = mo[:,nocc:]
max_memory = mycc.max_memory-lib.current_memory()[0]
blksize = min(nocc, max(2, int(max_memory*1e6/8/(nmo**3*2))))
max_memory = max(MEMORYMIN, max_memory)
fswap = lib.H5TmpFile()
ao2mo.kernel(mycc.mol, (orbo,mo,mo,mo), fswap,
max_memory=max_memory, verbose=log)
sym_forbid = orbspin[:,None] != orbspin
for p0, p1 in lib.prange(0, nocc, blksize):
tmp = np.asarray(fswap['eri_mo'][p0*nmo:p1*nmo])
tmp = lib.unpack_tril(tmp).reshape(p1-p0,nmo,nmo,nmo)
tmp[sym_forbid[p0:p1]] = 0
tmp[:,:,sym_forbid] = 0
eris.oooo[p0:p1] = (tmp[:,:nocc,:nocc,:nocc].transpose(0,2,1,3) -
tmp[:,:nocc,:nocc,:nocc].transpose(0,2,3,1))
eris.ooov[p0:p1] = (tmp[:,:nocc,:nocc,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,:nocc,:nocc].transpose(0,2,3,1))
eris.ovvv[p0:p1] = (tmp[:,nocc:,nocc:,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,nocc:,nocc:].transpose(0,2,3,1))
eris.oovv[p0:p1] = (tmp[:,nocc:,:nocc,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,:nocc,nocc:].transpose(0,2,3,1))
eris.ovov[p0:p1] = (tmp[:,:nocc,nocc:,nocc:].transpose(0,2,1,3) -
tmp[:,nocc:,nocc:,:nocc].transpose(0,2,3,1))
eris.ovvo[p0:p1] = (tmp[:,nocc:,nocc:,:nocc].transpose(0,2,1,3) -
tmp[:,:nocc,nocc:,nocc:].transpose(0,2,3,1))
tmp = None
cput0 = log.timer_debug1('transforming ovvv', *cput0)
eris.vvvv = feri.create_dataset('vvvv', (nvir,nvir,nvir,nvir), dtype)
sym_forbid = (orbspin[nocc:,None]!=orbspin[nocc:])[np.tril_indices(nvir)]
tril2sq = lib.square_mat_in_trilu_indices(nvir)
fswap = lib.H5TmpFile()
ao2mo.kernel(mycc.mol, orbv, fswap, max_memory=max_memory, verbose=log)
for p0, p1 in lib.prange(0, nvir, blksize):
off0 = p0*(p0+1)//2
off1 = p1*(p1+1)//2
tmp = np.asarray(fswap['eri_mo'][off0:off1])
tmp[sym_forbid[off0:off1]] = 0
tmp[:,sym_forbid] = 0
if p0 > 0:
c = tmp[ tril2sq[p0:p1,:p0] - off0 ]
c = lib.unpack_tril(c.reshape((p1-p0)*p0,-1))
eris.vvvv[p0:p1,:p0] = c.reshape(p1-p0,p0,nvir,nvir)
c = tmp[ tril2sq[:p1,p0:p1] - off0 ]
c = lib.unpack_tril(c.reshape((p1-p0)*p1,-1))
eris.vvvv[:p1,p0:p1] = c.reshape(p1,p1-p0,nvir,nvir)
tmp = None
for p0, p1 in lib.prange(0, nvir, blksize):
tmp = np.asarray(eris.vvvv[p0:p1])
eris.vvvv[p0:p1] = tmp.transpose(0,2,1,3) - tmp.transpose(0,2,3,1)
cput0 = log.timer_debug1('transforming vvvv', *cput0)
return eris
