def general(mol,
mo_coeffs,
erifile,
auxbasis='weigend+etb',
dataname='eri_mo',
tmpdir=None,
int3c='int3c2e',
aosym='s2ij',
int2c='int2c2e',
comp=1,
max_memory=MAX_MEMORY,
verbose=0,
compact=True):
''' Transform ij of (ij|L) to MOs.
'''
assert (aosym in ('s1', 's2ij'))
time0 = (time.clock(), time.time())
log = logger.new_logger(mol, verbose)
if tmpdir is None:
tmpdir = lib.param.TMPDIR
swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
cholesky_eri_b(mol,
swapfile.name,
auxbasis,
dataname,
int3c,
aosym,
int2c,
comp,
max_memory,
verbose=log)
fswap = h5py.File(swapfile.name, 'r')
time1 = log.timer('AO->MO eri transformation 1 pass', *time0)
nao = mo_coeffs[0].shape[0]
if aosym == 's1':
nao_pair = nao * nao
aosym_as_nr_e2 = 's1'
else:
nao_pair = nao * (nao + 1) // 2
aosym_as_nr_e2 = 's2kl'
ijmosym, nij_pair, moij, ijshape = \
ao2mo.incore._conc_mos(mo_coeffs[0], mo_coeffs[1],
compact and aosym != 's1')
naoaux = fswap['%s/0' % dataname].shape[-2]
feri = _create_h5file(erifile, dataname)
if comp == 1:
h5d_eri = feri.create_dataset(dataname, (naoaux, nij_pair), 'f8')
else:
h5d_eri = feri.create_dataset(dataname, (comp, naoaux, nij_pair), 'f8')
def save(row0, row1, buf):
if comp == 1:
h5d_eri[row0:row1] = buf
else:
h5d_eri[:, row0:row1] = buf
iolen = min(max(int(max_memory * .45e6 / 8 / (nao_pair + nij_pair)), 28),
naoaux)
totstep = (naoaux + iolen - 1) // iolen
ti0 = time1
with lib.call_in_background(save) as bsave:
for istep, (row0, row1) in enumerate(lib.prange(0, naoaux, iolen)):
nrow = row1 - row0
log.debug('step 2 [%d/%d], [%d:%d], row = %d', istep + 1, totstep,
row0, row1, nrow)
buf = _load_from_h5g(fswap[dataname], row0, row1)
if comp == 1:
buf = _ao2mo.nr_e2(buf, moij, ijshape, aosym_as_nr_e2, ijmosym)
bsave(row0, row1, buf)
else:
buf = _ao2mo.nr_e2(buf.reshape(comp * nrow, nao_pair), moij,
ijshape, aosym_as_nr_e2, ijmosym)
bsave(row0, row1, buf.reshape(comp, nrow, nij_pair))
buf = None
ti0 = log.timer(
'step 2 [%d/%d], [%d:%d], row = %d' %
(istep + 1, totstep, row0, row1, nrow), *ti0)
fswap.close()
feri.close()
log.timer('AO->MO CD eri transformation 2 pass', *time1)
log.timer('AO->MO CD eri transformation', *time0)
return erifile
def cholesky_eri(mol,
erifile,
auxbasis='weigend+etb',
dataname='j3c',
tmpdir=None,
int3c='int3c2e',
aosym='s2ij',
int2c='int2c2e',
comp=1,
max_memory=MAX_MEMORY,
auxmol=None,
verbose=logger.NOTE):
'''3-index density-fitting tensor.
'''
assert (aosym in ('s1', 's2ij'))
assert (comp == 1)
log = logger.new_logger(mol, verbose)
time0 = (time.clock(), time.time())
if auxmol is None:
auxmol = make_auxmol(mol, auxbasis)
if tmpdir is None:
tmpdir = lib.param.TMPDIR
swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
cholesky_eri_b(mol,
swapfile.name,
auxbasis,
dataname,
int3c,
aosym,
int2c,
comp,
max_memory,
auxmol,
verbose=log)
fswap = h5py.File(swapfile.name, 'r')
time1 = log.timer('generate (ij|L) 1 pass', *time0)
# Cannot let naoaux = auxmol.nao_nr() if auxbasis has linear dependence
nao = mol.nao_nr()
if aosym == 's1':
nao_pair = nao * nao
else:
nao_pair = nao * (nao + 1) // 2
feri = _create_h5file(erifile, dataname)
if comp == 1:
naoaux = fswap['%s/0' % dataname].shape[0]
h5d_eri = feri.create_dataset(dataname, (naoaux, nao_pair), 'f8')
else:
naoaux = fswap['%s/0' % dataname].shape[1]
h5d_eri = feri.create_dataset(dataname, (comp, naoaux, nao_pair), 'f8')
def save(row0, row1, buf):
if comp == 1:
h5d_eri[row0:row1] = buf
else:
h5d_eri[:, row0:row1] = buf
iolen = min(max(int(max_memory * .45e6 / 8 / nao_pair), 28), naoaux)
totstep = (naoaux + iolen - 1) // iolen
bufs1 = numpy.empty((iolen, nao_pair))
bufs2 = numpy.empty_like(bufs1)
ti0 = time1
with lib.call_in_background(save) as bsave:
for istep, (row0, row1) in enumerate(lib.prange(0, naoaux, iolen)):
nrow = row1 - row0
buf = _load_from_h5g(fswap[dataname], row0, row1, bufs1)
bufs1, bufs2 = bufs2, bufs1
bsave(row0, row1, buf)
ti0 = log.timer(
'step 2 [%d/%d], [%d:%d], row = %d' %
(istep + 1, totstep, row0, row1, nrow), *ti0)
fswap.close()
feri.close()
log.timer('cholesky_eri', *time0)
return erifile
def load(row_slice):
row0, row1 = row_slice
return _load_from_h5g(fswap[dataname], row0, row1)
def load(aux_slice):
b0, b1 = aux_slice
return _load_from_h5g(feri, b0, b1)
def load(start, stop, buf):
if start < stop:
_load_from_h5g(feri_swap, start, stop, buf)
def load(b0, b1, prefetch):
prefetch[0] = _load_from_h5g(feri, b0, b1)
def _make_eris_df(cc, mo_coeff=None):
eris = _RCCSD_ERIs(cc, mo_coeff)
nocc = eris.nocc
nmo = eris.fock.shape[0]
nvir = nmo - nocc
nocc_pair = nocc * (nocc + 1) // 2
nvir_pair = nvir * (nvir + 1) // 2
with_df = cc._scf.with_df
naux = eris.naux = with_df.get_naoaux()
eris.feri = lib.H5TmpFile()
eris.oovv = eris.feri.create_dataset('oovv', (nocc, nocc, nvir, nvir),
'f8')
eris.ovvv = eris.feri.create_dataset('ovvv', (nocc, nvir, nvir_pair), 'f8')
eris.vvL = eris.feri.create_dataset('vvL', (nvir_pair, naux), 'f8')
Loo = numpy.empty((naux, nocc, nocc))
Lov = numpy.empty((naux, nocc, nvir))
fswap = lib.H5TmpFile()
mo = numpy.asarray(eris.mo_coeff, order='F')
ijslice = (0, nmo, 0, nmo)
Lpqbuf = numpy.empty((with_df.blockdim, nmo, nmo))
vvbuf = numpy.empty((with_df.blockdim, nvir, nvir))
p1 = 0
for k, eri1 in enumerate(with_df.loop()):
Lpq = _ao2mo.nr_e2(eri1,
mo,
ijslice,
aosym='s2',
mosym='s1',
out=Lpqbuf)
p0, p1 = p1, p1 + Lpq.shape[0]
Lpq = Lpq.reshape(p1 - p0, nmo, nmo)
Loo[p0:p1] = Lpq[:, :nocc, :nocc]
Lov[p0:p1] = Lpq[:, :nocc, nocc:]
vvbuf[:p1 - p0] = Lpq[:, nocc:, nocc:]
Lvv = lib.pack_tril(vvbuf[:p1 - p0], out=Lpqbuf)
fswap[str(k)] = lib.transpose(Lvv, out=vvbuf)
Lpq = Lvv = Lpqbuf = vvbuf = None
Loo = Loo.reshape(naux, nocc**2)
Lov = Lov.reshape(naux, nocc * nvir)
eris.feri['oooo'] = lib.ddot(Loo.T, Loo).reshape(nocc, nocc, nocc, nocc)
eris.feri['ooov'] = lib.ddot(Loo.T, Lov).reshape(nocc, nocc, nocc, nvir)
eris.feri['ovoo'] = lib.ddot(Lov.T, Loo).reshape(nocc, nvir, nocc, nocc)
eris.feri['ovov'] = lib.ddot(Lov.T, Lov).reshape(nocc, nvir, nocc, nvir)
eris.oooo = eris.feri['oooo']
eris.ooov = eris.feri['ooov']
eris.ovoo = eris.feri['ovoo']
eris.ovov = eris.feri['ovov']
mem_now = lib.current_memory()[0]
max_memory = cc.max_memory - mem_now
blksize = max(
4, int(
(max_memory * .9e6 / 8 - nocc**2 * nvir_pair) / (nocc**2 + naux)))
oovv = numpy.empty((nocc, nocc, nvir_pair))
vvL = numpy.empty((blksize, naux))
for p0, p1 in lib.prange(0, nvir_pair, blksize):
outcore._load_from_h5g(fswap, p0, p1, vvL)
eris.vvL[p0:p1] = vvL[:p1 - p0]
oovv[:, :,
p0:p1] = lib.ddot(Loo.T,
vvL[:p1 - p0].T).reshape(nocc, nocc, p1 - p0)
oovv = lib.unpack_tril(oovv.reshape(nocc**2, nvir_pair))
eris.oovv[:] = oovv.reshape(nocc, nocc, nvir, nvir)
oovv = vvL = Loo = None
Lov = Lov.reshape(naux, nocc, nvir)
vblk = max(nocc, int((max_memory * .8e6 / 8) / (nocc * nvir_pair)))
vvblk = max(4, int((max_memory * .15e6 / 8) / (vblk * nocc + naux)))
ovvv = numpy.empty((nocc, vblk, nvir_pair))
for p0, p1 in lib.prange(0, nvir, vblk):
tmpLov = numpy.asarray(Lov[:, :, p0:p1].reshape(naux, -1), order='C')
for q0, q1 in lib.prange(0, nvir_pair, vvblk):
vvL = numpy.asarray(eris.vvL[q0:q1])
ovvv[:, :p1 - p0,
q0:q1] = lib.ddot(tmpLov.T,
vvL.T).reshape(nocc, p1 - p0, q1 - q0)
vvL = None
eris.ovvv[:, p0:p1] = ovvv[:, :p1 - p0]
return eris