def sr_loop(self, mol, auxmol, max_memory=2000):
'''Short range part'''
with addons.load(self._cderi, 'j3c') as j3c:
with addons.load(self._cderi, 'Lpq') as Lpq:
naoaux = j3c.shape[0]
for b0, b1 in self.prange(0, naoaux, self.blockdim):
yield (numpy.asarray(Lpq[b0:b1], order='C'),
numpy.asarray(j3c[b0:b1], order='C'))
def loop(self):
if self._cderi is None:
self.build()
with addons.load(self._cderi[0], 'j3c') as ferill:
naoaux = ferill.shape[0]
with addons.load(self._cderi[1], 'j3c') as feriss: # python2.6 not support multiple with
for b0, b1 in self.prange(0, naoaux, self.blockdim):
erill = numpy.asarray(ferill[b0:b1], order='C')
eriss = numpy.asarray(feriss[b0:b1], order='C')
yield erill, eriss
def loop(self):
if self._cderi is None:
self.build()
with addons.load(self._cderi[0], 'j3c') as ferill:
naoaux = ferill.shape[0]
with addons.load(
self._cderi[1],
'j3c') as feriss: # python2.6 not support multiple with
for b0, b1 in self.prange(0, naoaux, self.blockdim):
erill = numpy.asarray(ferill[b0:b1], order='C')
eriss = numpy.asarray(feriss[b0:b1], order='C')
yield erill, eriss
def get_naoaux(self):
# determine naoaux with self._cderi, because DF object may be used as CD
# object when self._cderi is provided.
if self._cderi is None:
self.build()
with addons.load(self._cderi, 'j3c') as feri:
return feri.shape[0]
def build(self):
t0 = (time.clock(), time.time())
log = logger.Logger(self.stdout, self.verbose)
mol = self.mol
auxmol = self.auxmol = incore.format_aux_basis(self.mol, self.auxbasis)
nao = mol.nao_nr()
naux = auxmol.nao_nr()
nao_pair = nao * (nao + 1) // 2
max_memory = (self.max_memory - lib.current_memory()[0]) * .8
if nao_pair * naux * 3 * 8 / 1e6 < max_memory:
self._cderi = incore.cholesky_eri(mol, auxmol=auxmol, verbose=log)
else:
if not isinstance(self._cderi, str):
if isinstance(self._cderi_file, str):
self._cderi = self._cderi_file
else:
self._cderi = self._cderi_file.name
outcore.cholesky_eri(mol,
self._cderi,
dataname='j3c',
auxmol=auxmol,
verbose=log)
if nao_pair * nao * 8 / 1e6 < max_memory:
with addons.load(self._cderi, 'j3c') as feri:
cderi = numpy.asarray(feri)
self._cderi = cderi
log.timer_debug1('Generate density fitting integrals', *t0)
return self
def get_naoaux(self):
# determine naoaux with self._cderi, because DF object may be used as CD
# object when self._cderi is provided.
if self._cderi is None:
self.build()
with addons.load(self._cderi, 'j3c') as feri:
return feri.shape[0]
def loop(self, blksize=None):
if self._cderi is None:
self.build()
if blksize is None:
blksize = self.blockdim
with addons.load(self._cderi, 'j3c') as feri:
if isinstance(feri, numpy.ndarray):
naoaux = feri.shape[0]
for b0, b1 in self.prange(0, naoaux, blksize):
yield numpy.asarray(feri[b0:b1], order='C')
else:
if isinstance(feri, h5py.Group):
# starting from pyscf-1.7, DF tensor may be stored in
# block format
naoaux = feri['0'].shape[0]
def load(aux_slice):
b0, b1 = aux_slice
return _load_from_h5g(feri, b0, b1)
else:
naoaux = feri.shape[0]
def load(aux_slice):
b0, b1 = aux_slice
return numpy.asarray(feri[b0:b1])
for dat in lib.map_with_prefetch(
load, self.prange(0, naoaux, blksize)):
yield dat
dat = None
def loop(self, blksize=None):
if self._cderi is None:
self.build()
if blksize is None:
blksize = self.blockdim
with addons.load(self._cderi, 'j3c') as feri:
if isinstance(feri, numpy.ndarray):
naoaux = feri.shape[0]
for b0, b1 in self.prange(0, naoaux, blksize):
yield numpy.asarray(feri[b0:b1], order='C')
else:
if isinstance(feri, h5py.Group):
# starting from pyscf-1.7, DF tensor may be stored in
# block format
naoaux = feri['0'].shape[0]
def load(b0, b1, prefetch):
prefetch[0] = _load_from_h5g(feri, b0, b1)
else:
naoaux = feri.shape[0]
def load(b0, b1, prefetch):
prefetch[0] = numpy.asarray(feri[b0:b1])
dat = [None]
prefetch = [None]
with lib.call_in_background(load) as bload:
bload(0, min(blksize, naoaux), prefetch)
for b0, b1 in self.prange(blksize, naoaux, blksize):
dat, prefetch = prefetch, dat
bload(b0, b1, prefetch)
yield dat[0]
yield prefetch[0]
def build(self):
t0 = (time.clock(), time.time())
log = logger.Logger(self.stdout, self.verbose)
mol = self.mol
auxmol = self.auxmol = incore.format_aux_basis(self.mol, self.auxbasis)
nao = mol.nao_nr()
naux = auxmol.nao_nr()
nao_pair = nao*(nao+1)//2
max_memory = (self.max_memory - lib.current_memory()[0]) * .8
if nao_pair*naux*3*8/1e6 < max_memory:
self._cderi = incore.cholesky_eri(mol, auxmol=auxmol, verbose=log)
else:
if not isinstance(self._cderi, str):
if isinstance(self._cderi_file, str):
self._cderi = self._cderi_file
else:
self._cderi = self._cderi_file.name
outcore.cholesky_eri(mol, self._cderi, auxmol=auxmol, verbose=log)
if nao_pair*nao*8/1e6 < max_memory:
with addons.load(self._cderi) as feri:
cderi = numpy.asarray(feri)
self._cderi = cderi
log.timer_debug1('Generate density fitting integrals', *t0)
return self
def loop(self):
if self._cderi is None:
self.build()
with addons.load(self._cderi) as feri:
naoaux = feri.shape[0]
for b0, b1 in self.prange(0, naoaux, self.blockdim):
eri1 = numpy.asarray(feri[b0:b1], order='C')
yield eri1
def loop(self):
if self._cderi is None:
self.build()
with addons.load(self._cderi, 'j3c') as feri:
naoaux = feri.shape[0]
for b0, b1 in self.prange(0, naoaux, self.blockdim):
eri1 = numpy.asarray(feri[b0:b1], order='C')
yield eri1
def loop(self, blksize=None):
if self._cderi is None:
self.build()
if blksize is None:
blksize = self.blockdim
with addons.load(self._cderi, 'j3c') as feri:
naoaux = feri.shape[0]
for b0, b1 in self.prange(0, naoaux, blksize):
eri1 = numpy.asarray(feri[b0:b1], order='C')
yield eri1
def get_naoaux(self):
# determine naoaux with self._cderi, because DF object may be used as CD
# object when self._cderi is provided.
if self._cderi is None:
self.build()
with addons.load(self._cderi, 'j3c') as feri:
if isinstance(feri, h5py.Group):
return feri['0'].shape[0]
else:
return feri.shape[0]
def build(self):
t0 = (time.clock(), time.time())
log = logger.Logger(self.stdout, self.verbose)
self.check_sanity()
self.dump_flags()
mol = self.mol
auxmol = self.auxmol = addons.make_auxmol(self.mol, self.auxbasis)
nao = mol.nao_nr()
naux = auxmol.nao_nr()
nao_pair = nao * (nao + 1) // 2
max_memory = (self.max_memory - lib.current_memory()[0]) * .8
int3c = mol._add_suffix('int3c2e')
int2c = mol._add_suffix('int2c2e')
if (nao_pair * naux * 3 * 8 / 1e6 < max_memory
and not isinstance(self._cderi_to_save, str)):
self._cderi = incore.cholesky_eri(mol,
int3c=int3c,
int2c=int2c,
auxmol=auxmol,
verbose=log)
else:
if isinstance(self._cderi_to_save, str):
cderi = self._cderi_to_save
else:
cderi = self._cderi_to_save.name
if isinstance(self._cderi, str):
log.warn(
'Value of _cderi is ignored. DF integrals will be '
'saved in file %s .', cderi)
outcore.cholesky_eri(mol,
cderi,
dataname='j3c',
int3c=int3c,
int2c=int2c,
auxmol=auxmol,
max_memory=max_memory,
verbose=log)
if nao_pair * naux * 8 / 1e6 < max_memory:
with addons.load(cderi, 'j3c') as feri:
cderi = numpy.asarray(feri)
self._cderi = cderi
log.timer_debug1('Generate density fitting integrals', *t0)
return self
def build(self):
t0 = (time.clock(), time.time())
log = logger.Logger(self.stdout, self.verbose)
self.check_sanity()
self.dump_flags()
mol = self.mol
auxmol = self.auxmol = addons.make_auxmol(self.mol, self.auxbasis)
nao = mol.nao_nr()
naux = auxmol.nao_nr()
nao_pair = nao*(nao+1)//2
max_memory = (self.max_memory - lib.current_memory()[0]) * .8
int3c = mol._add_suffix('int3c2e')
int2c = mol._add_suffix('int2c2e')
if (nao_pair*naux*3*8/1e6 < max_memory and
not isinstance(self._cderi_to_save, str)):
self._cderi = incore.cholesky_eri(mol, int3c=int3c, int2c=int2c,
auxmol=auxmol, verbose=log)
else:
if isinstance(self._cderi_to_save, str):
cderi = self._cderi_to_save
else:
cderi = self._cderi_to_save.name
if isinstance(self._cderi, str):
log.warn('Value of _cderi is ignored. DF integrals will be '
'saved in file %s .', cderi)
outcore.cholesky_eri(mol, cderi, dataname='j3c',
int3c=int3c, int2c=int2c, auxmol=auxmol,
max_memory=max_memory, verbose=log)
if nao_pair*naux*8/1e6 < max_memory:
with addons.load(cderi, 'j3c') as feri:
cderi = numpy.asarray(feri)
self._cderi = cderi
log.timer_debug1('Generate density fitting integrals', *t0)
return self
def get_naoaux(self):
'''The dimension of auxiliary basis at gamma point'''
# determine naoaux with self._cderi, because DF object may be used as CD
# object when self._cderi is provided.
if self._cderi is None:
self.build()
# self._cderi['j3c/k_id/seg_id']
with addons.load(self._cderi, 'j3c/0') as feri:
if isinstance(feri, h5py.Group):
naux = feri['0'].shape[0]
else:
naux = feri.shape[0]
cell = self.cell
if (cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum' and
not isinstance(self._cderi, numpy.ndarray)):
with h5py.File(self._cderi, 'r') as feri:
if 'j3c-/0' in feri:
dat = feri['j3c-/0']
if isinstance(dat, h5py.Group):
naux += dat['0'].shape[0]
else:
naux += dat.shape[0]
return naux
def get_naoaux(self):
'''The dimension of auxiliary basis at gamma point'''
# determine naoaux with self._cderi, because DF object may be used as CD
# object when self._cderi is provided.
if self._cderi is None:
self.build()
# self._cderi['j3c/k_id/seg_id']
with addons.load(self._cderi, 'j3c/0') as feri:
if isinstance(feri, h5py.Group):
naux = feri['0'].shape[0]
else:
naux = feri.shape[0]
cell = self.cell
if (cell.dimension == 2 and cell.low_dim_ft_type != 'inf_vacuum'
and not isinstance(self._cderi, numpy.ndarray)):
with h5py.File(self._cderi, 'r') as feri:
if 'j3c-/0' in feri:
dat = feri['j3c-/0']
if isinstance(dat, h5py.Group):
naux += dat['0'].shape[0]
else:
naux += dat.shape[0]
return naux
def load(self, key):
return addons.load(self._cderi, key)
