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 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 build(self):
t0 = (logger.process_clock(), logger.perf_counter())
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]
int3c = mol._add_suffix('int3c2e')
int2c = mol._add_suffix('int2c2e')
if (nao_pair * naux * 8 / 1e6 < .9 * max_memory
and not isinstance(self._cderi_to_save, str)):
self._cderi = incore.cholesky_eri(mol,
int3c=int3c,
int2c=int2c,
auxmol=auxmol,
max_memory=max_memory,
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):
# If cderi needs to be saved in
log.warn(
'Value of _cderi is ignored. DF integrals will be '
'saved in file %s .', cderi)
if self._compatible_format or isinstance(self._cderi_to_save, str):
outcore.cholesky_eri(mol,
cderi,
dataname='j3c',
int3c=int3c,
int2c=int2c,
auxmol=auxmol,
max_memory=max_memory,
verbose=log)
else:
# Store DF tensor in blocks. This is to reduce the
# initiailzation overhead
outcore.cholesky_eri_b(mol,
cderi,
dataname='j3c',
int3c=int3c,
int2c=int2c,
auxmol=auxmol,
max_memory=max_memory,
verbose=log)
self._cderi = cderi
log.timer_debug1('Generate density fitting integrals', *t0)
return self
def cholesky_eri(mol,
auxbasis='weigend+etb',
auxmol=None,
int3c='int3c2e_spinor',
aosym='s1',
int2c='int2c2e_sph',
comp=1,
verbose=0):
return incore.cholesky_eri(mol, auxbasis, auxmol, int3c, aosym, int2c,
comp, verbose, aux_e2)
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
else:
return 's' + sym
if __name__ == '__main__':
mol = pyscf.gto.Mole()
mol.verbose = 0
mol.output = None
mol.atom = [
["O" , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
[1 , (0. , 0.757 , 0.587)]]
mol.basis = 'cc-pvtz'
mol.build()
cderi0 = incore.cholesky_eri(mol)
cholesky_eri(mol, 'cderi.dat')
with h5py.File('cderi.dat') as feri:
print(numpy.allclose(feri['eri_mo'], cderi0))
cholesky_eri(mol, 'cderi.dat', ioblk_size=.5)
with h5py.File('cderi.dat') as feri:
print(numpy.allclose(feri['eri_mo'], cderi0))
general(mol, (numpy.eye(mol.nao_nr()),)*2, 'cderi.dat',
max_memory=.5, ioblk_size=.2, verbose=6)
with h5py.File('cderi.dat') as feri:
print(numpy.allclose(feri['eri_mo'], cderi0))
del (MAX_MEMORY)
if __name__ == '__main__':
from pyscf.df import incore
mol = gto.Mole()
mol.verbose = 0
mol.output = None
mol.atom = [["O", (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.basis = 'cc-pvtz'
mol.build()
cderi0 = incore.cholesky_eri(mol)
cholesky_eri(mol, 'cderi.dat')
with h5py.File('cderi.dat') as feri:
print(numpy.allclose(feri['j3c'], cderi0))
cholesky_eri(mol, 'cderi.dat', ioblk_size=.5)
with h5py.File('cderi.dat') as feri:
print(numpy.allclose(feri['j3c'], cderi0))
general(mol, (numpy.eye(mol.nao_nr()), ) * 2,
'cderi.dat',
max_memory=.5,
ioblk_size=.2,
verbose=6)
with h5py.File('cderi.dat') as feri:
print(numpy.allclose(feri['j3c'], cderi0))
def cholesky_eri(mol, auxbasis='weigend+etb', auxmol=None,
int3c='int3c2e_spinor', aosym='s1', int2c='int2c2e_sph', comp=1,
verbose=0):
return incore.cholesky_eri(mol, auxbasis, auxmol, int3c, aosym, int2c,
comp, verbose, aux_e2)