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 cholesky_eri(mol, auxbasis='weigend+etb', aosym='s1', verbose=0):
t0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
auxmol = incore.format_aux_basis(mol, auxbasis)
j2c = incore.fill_2c2e(mol, auxmol)
log.debug('size of aux basis %d', j2c.shape[0])
t1 = log.timer('2c2e', *t0)
low = scipy.linalg.cholesky(j2c, lower=True)
j2c = None
t1 = log.timer('Cholesky 2c2e', *t1)
j3c_ll = aux_e2(mol, auxmol, intor='cint3c2e_spinor', aosym=aosym)
j3c_ss = aux_e2(mol, auxmol, intor='cint3c2e_spsp1_spinor', aosym=aosym)
t1 = log.timer('3c2e', *t1)
cderi_ll = scipy.linalg.solve_triangular(low, j3c_ll.T, lower=True,
overwrite_b=True)
cderi_ss = scipy.linalg.solve_triangular(low, j3c_ss.T, lower=True,
overwrite_b=True)
# solve_triangular return cderi in Fortran order
cderi = (pyscf.lib.transpose(cderi_ll.T),
pyscf.lib.transpose(cderi_ss.T))
log.timer('cholesky_eri', *t0)
return cderi
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 cholesky_eri(mol, auxbasis='weigend+etb', aosym='s1', verbose=0):
t0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
auxmol = incore.format_aux_basis(mol, auxbasis)
j2c = incore.fill_2c2e(mol, auxmol)
log.debug('size of aux basis %d', j2c.shape[0])
t1 = log.timer('2c2e', *t0)
low = scipy.linalg.cholesky(j2c, lower=True)
j2c = None
t1 = log.timer('Cholesky 2c2e', *t1)
j3c_ll = aux_e2(mol, auxmol, intor='cint3c2e_spinor', aosym=aosym)
j3c_ss = aux_e2(mol, auxmol, intor='cint3c2e_spsp1_spinor', aosym=aosym)
t1 = log.timer('3c2e', *t1)
cderi_ll = scipy.linalg.solve_triangular(low,
j3c_ll.T,
lower=True,
overwrite_b=True)
cderi_ss = scipy.linalg.solve_triangular(low,
j3c_ss.T,
lower=True,
overwrite_b=True)
# solve_triangular return cderi in Fortran order
cderi = (pyscf.lib.transpose(cderi_ll.T), pyscf.lib.transpose(cderi_ss.T))
log.timer('cholesky_eri', *t0)
return cderi
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)
n2c = mol.nao_2c()
naux = auxmol.nao_nr()
nao_pair = n2c*(n2c+1)//2
max_memory = (self.max_memory - lib.current_memory()[0]) * .8
if nao_pair*naux*3*16/1e6*2 < max_memory:
self._cderi = r_incore.cholesky_eri(mol, auxbasis=self.auxbasis,
aosym='s2', verbose=log)
else:
raise NotImplementedError
self._cderifile = self._cderi
self._cderi = r_outcore.cholesky_eri(mol, self._cderi.name,
auxbasis=self.auxbasis,
verbose=log)
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)
n2c = mol.nao_2c()
naux = auxmol.nao_nr()
nao_pair = n2c * (n2c + 1) // 2
max_memory = (self.max_memory - lib.current_memory()[0]) * .8
if nao_pair * naux * 3 * 16 / 1e6 * 2 < max_memory:
self._cderi = r_incore.cholesky_eri(mol,
auxbasis=self.auxbasis,
aosym='s2',
verbose=log)
else:
raise NotImplementedError
self._cderifile = self._cderi
self._cderi = r_outcore.cholesky_eri(mol,
self._cderi.name,
auxbasis=self.auxbasis,
verbose=log)
return self
def general(mol, mo_coeffs, erifile, auxbasis='weigend+etb', dataname='eri_mo', tmpdir=None,
int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph', comp=1,
max_memory=2000, ioblk_size=256, verbose=0, compact=True):
''' Transform ij of (ij|L) to MOs.
'''
assert(aosym in ('s1', 's2ij'))
assert(comp == 1)
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
cholesky_eri_b(mol, swapfile.name, auxbasis, dataname,
int3c, aosym, int2c, comp, ioblk_size, verbose=log)
fswap = h5py.File(swapfile.name, 'r')
time1 = log.timer('AO->MO eri transformation 1 pass', *time0)
ijsame = compact and iden_coeffs(mo_coeffs[0], mo_coeffs[1])
nmoi = mo_coeffs[0].shape[1]
nmoj = mo_coeffs[1].shape[1]
nao = mo_coeffs[0].shape[0]
auxmol = incore.format_aux_basis(mol, auxbasis)
naoaux = auxmol.nao_nr()
aosym = _stand_sym_code(aosym)
if aosym == 's1':
nao_pair = nao * nao
aosym_as_nr_e2 = 's1'
else:
nao_pair = nao * (nao+1) // 2
aosym_as_nr_e2 = 's2kl'
if compact and ijsame and aosym != 's1':
log.debug('i-mo == j-mo')
ijmosym = 's2'
nij_pair = nmoi*(nmoi+1) // 2
moij = numpy.asarray(mo_coeffs[0], order='F')
ijshape = (0, nmoi, 0, nmoi)
else:
ijmosym = 's1'
nij_pair = nmoi*nmoj
moij = numpy.asarray(numpy.hstack((mo_coeffs[0],mo_coeffs[1])), order='F')
ijshape = (0, nmoi, nmoi, nmoj)
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
if comp == 1:
chunks = (min(int(16e3/nmoj),naoaux), nmoj) # 128K
h5d_eri = feri.create_dataset(dataname, (naoaux,nij_pair), 'f8',
chunks=chunks)
aopairblks = len(fswap[dataname])
else:
chunks = (1, min(int(16e3/nmoj),naoaux), nmoj) # 128K
h5d_eri = feri.create_dataset(dataname, (comp,naoaux,nij_pair), 'f8',
chunks=chunks)
aopairblks = len(fswap[dataname+'/0'])
if comp > 1:
for icomp in range(comp):
feri.create_group(str(icomp)) # for h5py old version
iolen = min(int(ioblk_size*1e6/8/(nao_pair+nij_pair)), naoaux)
totstep = (naoaux+iolen-1)//iolen * comp
buf = numpy.empty((iolen, nao_pair))
istep = 0
ti0 = time1
for icomp in range(comp):
for row0, row1 in prange(0, naoaux, iolen):
nrow = row1 - row0
istep += 1
log.debug('step 2 [%d/%d], [%d,%d:%d], row = %d',
istep, totstep, icomp, row0, row1, nrow)
col0 = 0
for ic in range(aopairblks):
if comp == 1:
dat = fswap['%s/%d'%(dataname,ic)]
else:
dat = fswap['%s/%d/%d'%(dataname,icomp,ic)]
col1 = col0 + dat.shape[1]
buf[:nrow,col0:col1] = dat[row0:row1]
col0 = col1
buf1 = _ao2mo.nr_e2_(buf[:nrow], moij, ijshape, aosym_as_nr_e2, ijmosym)
if comp == 1:
h5d_eri[row0:row1] = buf1
else:
h5d_eri[icomp,row0:row1] = buf1
ti0 = log.timer('step 2 [%d/%d], [%d,%d:%d], row = %d'%
(istep, totstep, icomp, 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_b(mol, erifile, auxbasis='weigend+etb', dataname='eri_mo',
int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph',
comp=1, ioblk_size=256, verbose=logger.NOTE):
'''3-center 2-electron AO integrals
'''
assert(aosym in ('s1', 's2ij'))
assert(comp == 1)
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
auxmol = incore.format_aux_basis(mol, auxbasis)
j2c = incore.fill_2c2e(mol, auxmol, intor=int2c)
log.debug('size of aux basis %d', j2c.shape[0])
time1 = log.timer('2c2e', *time0)
low = scipy.linalg.cholesky(j2c, lower=True)
j2c = None
time1 = log.timer('Cholesky 2c2e', *time1)
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
if comp > 1:
for icomp in range(comp):
feri.create_group(str(icomp)) # for h5py old version
atm, bas, env = \
pyscf.gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
c_atm = numpy.asarray(atm, dtype=numpy.int32, order='C')
c_bas = numpy.asarray(bas, dtype=numpy.int32, order='C')
c_env = numpy.asarray(env, dtype=numpy.double, order='C')
natm = ctypes.c_int(mol.natm+auxmol.natm)
nbas = ctypes.c_int(mol.nbas)
if 'ssc' in int3c:
ao_loc = _ri.make_loc(0, mol.nbas, bas)
kloc = _ri.make_loc(mol.nbas, auxmol.nbas, bas, True)
elif 'cart' in int3c:
ao_loc = _ri.make_loc(0, mol.nbas, bas, True)
kloc = _ri.make_loc(mol.nbas, auxmol.nbas, bas, True)
else:
ao_loc = _ri.make_loc(0, mol.nbas, bas)
kloc = _ri.make_loc(mol.nbas, auxmol.nbas, bas)
nao = ao_loc[-1] - ao_loc[0]
naoaux = kloc[-1] - kloc[0]
if aosym == 's1':
nao_pair = nao * nao
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's1')
else:
nao_pair = nao * (nao+1) // 2
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's2ij')
log.debug('erifile %.8g MB, IO buf size %.8g MB',
naoaux*nao_pair*8/1e6, comp*buflen*naoaux*8/1e6)
if log.verbose >= logger.DEBUG1:
log.debug1('shranges = %s', shranges)
cintopt = _vhf.make_cintopt(c_atm, c_bas, c_env, int3c)
bufs1 = numpy.empty((comp*max([x[2] for x in shranges]),naoaux))
for istep, sh_range in enumerate(shranges):
log.debug('int3c2e [%d/%d], AO [%d:%d], nrow = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, nrow = sh_range
basrange = (bstart, bend-bstart, 0, mol.nbas, mol.nbas, auxmol.nbas)
buf = bufs1[:comp*nrow].reshape(comp,nrow,naoaux)
if 's1' in aosym:
ijkoff = ao_loc[bstart] * nao * naoaux
else:
ijkoff = ao_loc[bstart] * (ao_loc[bstart]+1) // 2 * naoaux
_ri.nr_auxe2(int3c, basrange,
atm, bas, env, aosym, comp, cintopt, buf, ijkoff,
ao_loc[bend]-ao_loc[bstart],
nao, naoaux, ao_loc[bstart:bend+1], ao_loc, kloc)
for icomp in range(comp):
if comp == 1:
label = '%s/%d'%(dataname,istep)
else:
label = '%s/%d/%d'%(dataname,icomp,istep)
cderi = scipy.linalg.solve_triangular(low, buf[icomp].T,
lower=True, overwrite_b=True)
feri[label] = cderi
time1 = log.timer('gen CD eri [%d/%d]' % (istep+1,len(shranges)), *time1)
buf = bufs1 = None
feri.close()
_ri.libri.CINTdel_optimizer(ctypes.byref(cintopt))
return erifile
def cholesky_eri(mol, erifile, auxbasis='weigend+etb', dataname='eri_mo', tmpdir=None,
int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph', comp=1,
ioblk_size=256, auxmol=None, verbose=0):
'''3-center 2-electron AO integrals
'''
assert(aosym in ('s1', 's2ij'))
assert(comp == 1)
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
if auxmol is None:
auxmol = incore.format_aux_basis(mol, auxbasis)
swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
cholesky_eri_b(mol, swapfile.name, auxbasis, dataname,
int3c, aosym, int2c, comp, ioblk_size, verbose=log)
fswap = h5py.File(swapfile.name, 'r')
time1 = log.timer('generate (ij|L) 1 pass', *time0)
nao = mol.nao_nr()
naoaux = auxmol.nao_nr()
aosym = _stand_sym_code(aosym)
if aosym == 's1':
nao_pair = nao * nao
else:
nao_pair = nao * (nao+1) // 2
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
if comp == 1:
chunks = (min(int(16e3/nao),naoaux), nao) # 128K
h5d_eri = feri.create_dataset(dataname, (naoaux,nao_pair), 'f8',
chunks=chunks)
else:
chunks = (1, min(int(16e3/nao),naoaux), nao) # 128K
h5d_eri = feri.create_dataset(dataname, (comp,naoaux,nao_pair), 'f8',
chunks=chunks)
aopairblks = len(fswap[dataname+'/0'])
iolen = min(int(ioblk_size*1e6/8/nao_pair), naoaux)
totstep = (naoaux+iolen-1)//iolen * comp
buf = numpy.empty((iolen, nao_pair))
ti0 = time1
for icomp in range(comp):
istep = 0
for row0, row1 in prange(0, naoaux, iolen):
nrow = row1 - row0
istep += 1
col0 = 0
for ic in range(aopairblks):
dat = fswap['%s/%d/%d'%(dataname,icomp,ic)]
col1 = col0 + dat.shape[1]
buf[:nrow,col0:col1] = dat[row0:row1]
col0 = col1
if comp == 1:
h5d_eri[row0:row1] = buf[:nrow]
else:
h5d_eri[icomp,row0:row1] = buf[:nrow]
ti0 = log.timer('step 2 [%d/%d], [%d,%d:%d], row = %d'%
(istep, totstep, icomp, row0, row1, nrow), *ti0)
fswap.close()
feri.close()
log.timer('cholesky_eri', *time0)
return erifile
def cholesky_eri_b(mol, erifile, auxbasis='weigend+etb', dataname='eri_mo',
int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph',
comp=1, ioblk_size=256, verbose=logger.NOTE):
'''3-center 2-electron AO integrals
'''
assert(aosym in ('s1', 's2ij'))
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
auxmol = incore.format_aux_basis(mol, auxbasis)
j2c = incore.fill_2c2e(mol, auxmol, intor=int2c)
log.debug('size of aux basis %d', j2c.shape[0])
time1 = log.timer('2c2e', *time0)
low = scipy.linalg.cholesky(j2c, lower=True)
j2c = None
time1 = log.timer('Cholesky 2c2e', *time1)
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
for icomp in range(comp):
feri.create_group('%s/%d'%(dataname,icomp)) # for h5py old version
def store(b, label):
cderi = scipy.linalg.solve_triangular(low, b, lower=True, overwrite_b=True)
if cderi.flags.f_contiguous:
cderi = lib.transpose(cderi.T)
feri[label] = cderi
atm, bas, env, ao_loc = incore._env_and_aoloc(int3c, mol, auxmol)
nao = ao_loc[mol.nbas]
naoaux = ao_loc[-1] - nao
if aosym == 's1':
nao_pair = nao * nao
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's1')
else:
nao_pair = nao * (nao+1) // 2
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's2ij')
log.debug('erifile %.8g MB, IO buf size %.8g MB',
naoaux*nao_pair*8/1e6, comp*buflen*naoaux*8/1e6)
if log.verbose >= logger.DEBUG1:
log.debug1('shranges = %s', shranges)
cintopt = gto.moleintor.make_cintopt(atm, bas, env, int3c)
bufs1 = numpy.empty((comp*max([x[2] for x in shranges]),naoaux))
for istep, sh_range in enumerate(shranges):
log.debug('int3c2e [%d/%d], AO [%d:%d], nrow = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, nrow = sh_range
shls_slice = (bstart, bend, 0, mol.nbas, mol.nbas, mol.nbas+auxmol.nbas)
buf = _ri.nr_auxe2(int3c, atm, bas, env, shls_slice, ao_loc,
aosym, comp, cintopt, bufs1)
if comp == 1:
store(buf.T, '%s/0/%d'%(dataname,istep))
else:
for icomp in range(comp):
store(buf[icomp].T, '%s/%d/%d'%(dataname,icomp,istep))
time1 = log.timer('gen CD eri [%d/%d]' % (istep+1,len(shranges)), *time1)
buf = bufs1 = None
feri.close()
return erifile
def cholesky_eri_b(mol, erifile, auxbasis='weigend', dataname='eri_mo',
int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph',
comp=1, ioblk_size=256, verbose=logger.NOTE):
assert(aosym in ('s1', 's2ij'))
assert(comp == 1)
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
auxmol = incore.format_aux_basis(mol, auxbasis)
j2c = incore.fill_2c2e(mol, auxmol, intor=int2c)
log.debug('size of aux basis %d', j2c.shape[0])
time1 = log.timer('2c2e', *time0)
low = scipy.linalg.cholesky(j2c, lower=True)
j2c = None
time1 = log.timer('Cholesky 2c2e', *time1)
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
if comp > 1:
for icomp in range(comp):
feri.create_group(str(icomp)) # for h5py old version
nao = mol.nao_nr()
naoaux = auxmol.nao_nr()
if aosym == 's1':
fill = _fpointer('RIfill_s1_auxe2')
nao_pair = nao * nao
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's1')
else:
fill = _fpointer('RIfill_s2ij_auxe2')
nao_pair = nao * (nao+1) // 2
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's2ij')
log.debug('erifile %.8g MB, IO buf size %.8g MB',
naoaux*nao_pair*8/1e6, comp*buflen*naoaux*8/1e6)
log.debug1('shranges = %s', shranges)
atm, bas, env = \
pyscf.gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
c_atm = numpy.array(atm, dtype=numpy.int32)
c_bas = numpy.array(bas, dtype=numpy.int32)
c_env = numpy.array(env)
natm = ctypes.c_int(mol.natm)
nbas = ctypes.c_int(mol.nbas)
fintor = _fpointer(int3c)
cintopt = _vhf.make_cintopt(c_atm, c_bas, c_env, int3c)
for istep, sh_range in enumerate(shranges):
log.debug('int3c2e [%d/%d], AO [%d:%d], nrow = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, nrow = sh_range
buf = numpy.empty((comp,nrow,naoaux))
libri.RInr_3c2e_auxe2_drv(fintor, fill,
buf.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(bstart), ctypes.c_int(bend-bstart),
ctypes.c_int(mol.nbas), ctypes.c_int(auxmol.nbas),
ctypes.c_int(comp), cintopt,
c_atm.ctypes.data_as(ctypes.c_void_p), natm,
c_bas.ctypes.data_as(ctypes.c_void_p), nbas,
c_env.ctypes.data_as(ctypes.c_void_p))
for icomp in range(comp):
if comp == 1:
label = '%s/%d'%(dataname,istep)
else:
label = '%s/%d/%d'%(dataname,icomp,istep)
cderi = scipy.linalg.solve_triangular(low, buf[icomp].T,
lower=True, overwrite_b=True)
feri[label] = cderi
time1 = log.timer('gen CD eri [%d/%d]' % (istep+1,len(shranges)), *time1)
feri.close()
libri.CINTdel_optimizer(ctypes.byref(cintopt))
return erifile
def cholesky_eri_b(mol, erifile, auxbasis='weigend+etb', dataname='eri_mo',
int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph',
comp=1, ioblk_size=256, verbose=logger.NOTE):
'''3-center 2-electron AO integrals
'''
assert(aosym in ('s1', 's2ij'))
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
auxmol = incore.format_aux_basis(mol, auxbasis)
j2c = incore.fill_2c2e(mol, auxmol, intor=int2c)
log.debug('size of aux basis %d', j2c.shape[0])
time1 = log.timer('2c2e', *time0)
low = scipy.linalg.cholesky(j2c, lower=True)
j2c = None
time1 = log.timer('Cholesky 2c2e', *time1)
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
for icomp in range(comp):
feri.create_group('%s/%d'%(dataname,icomp)) # for h5py old version
def store(b, label):
cderi = scipy.linalg.solve_triangular(low, b, lower=True, overwrite_b=True)
if cderi.flags.f_contiguous:
cderi = lib.transpose(cderi.T)
feri[label] = cderi
atm, bas, env, ao_loc = incore._env_and_aoloc(int3c, mol, auxmol)
nao = ao_loc[mol.nbas]
naoaux = ao_loc[-1] - nao
if aosym == 's1':
nao_pair = nao * nao
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's1')
else:
nao_pair = nao * (nao+1) // 2
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's2ij')
log.debug('erifile %.8g MB, IO buf size %.8g MB',
naoaux*nao_pair*8/1e6, comp*buflen*naoaux*8/1e6)
if log.verbose >= logger.DEBUG1:
log.debug1('shranges = %s', shranges)
cintopt = gto.moleintor.make_cintopt(atm, bas, env, int3c)
bufs1 = numpy.empty((comp*max([x[2] for x in shranges]),naoaux))
for istep, sh_range in enumerate(shranges):
log.debug('int3c2e [%d/%d], AO [%d:%d], nrow = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, nrow = sh_range
shls_slice = (bstart, bend, 0, mol.nbas, mol.nbas, mol.nbas+auxmol.nbas)
buf = _ri.nr_auxe2(int3c, atm, bas, env, shls_slice, ao_loc,
aosym, comp, cintopt, bufs1)
if comp == 1:
store(buf.T, '%s/0/%d'%(dataname,istep))
else:
for icomp in range(comp):
store(buf[icomp].T, '%s/%d/%d'%(dataname,icomp,istep))
time1 = log.timer('gen CD eri [%d/%d]' % (istep+1,len(shranges)), *time1)
buf = bufs1 = None
feri.close()
return erifile
def cholesky_eri(
mol,
erifile,
auxbasis="weigend+etb",
dataname="eri_mo",
tmpdir=None,
int3c="cint3c2e_sph",
aosym="s2ij",
int2c="cint2c2e_sph",
comp=1,
ioblk_size=256,
auxmol=None,
verbose=0,
):
"""3-center 2-electron AO integrals
"""
assert aosym in ("s1", "s2ij")
assert comp == 1
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
if auxmol is None:
auxmol = incore.format_aux_basis(mol, auxbasis)
swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
cholesky_eri_b(mol, swapfile.name, auxbasis, dataname, int3c, aosym, int2c, comp, ioblk_size, verbose=log)
fswap = h5py.File(swapfile.name, "r")
time1 = log.timer("generate (ij|L) 1 pass", *time0)
nao = mol.nao_nr()
naoaux = auxmol.nao_nr()
aosym = _stand_sym_code(aosym)
if aosym == "s1":
nao_pair = nao * nao
else:
nao_pair = nao * (nao + 1) // 2
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del (feri[dataname])
else:
feri = h5py.File(erifile, "w")
if comp == 1:
chunks = (min(int(16e3 / nao), naoaux), nao) # 128K
h5d_eri = feri.create_dataset(dataname, (naoaux, nao_pair), "f8", chunks=chunks)
else:
chunks = (1, min(int(16e3 / nao), naoaux), nao) # 128K
h5d_eri = feri.create_dataset(dataname, (comp, naoaux, nao_pair), "f8", chunks=chunks)
aopairblks = len(fswap[dataname + "/0"])
iolen = min(int(ioblk_size * 1e6 / 8 / nao_pair), naoaux)
totstep = (naoaux + iolen - 1) // iolen * comp
buf = numpy.empty((iolen, nao_pair))
ti0 = time1
for icomp in range(comp):
istep = 0
for row0, row1 in prange(0, naoaux, iolen):
nrow = row1 - row0
istep += 1
col0 = 0
for ic in range(aopairblks):
dat = fswap["%s/%d/%d" % (dataname, icomp, ic)]
col1 = col0 + dat.shape[1]
buf[:nrow, col0:col1] = dat[row0:row1]
col0 = col1
if comp == 1:
h5d_eri[row0:row1] = buf[:nrow]
else:
h5d_eri[icomp, row0:row1] = buf[:nrow]
ti0 = log.timer("step 2 [%d/%d], [%d,%d:%d], row = %d" % (istep, totstep, icomp, row0, row1, nrow), *ti0)
fswap.close()
feri.close()
log.timer("cholesky_eri", *time0)
return erifile
def general(
mol,
mo_coeffs,
erifile,
auxbasis="weigend+etb",
dataname="eri_mo",
tmpdir=None,
int3c="cint3c2e_sph",
aosym="s2ij",
int2c="cint2c2e_sph",
comp=1,
max_memory=2000,
ioblk_size=256,
verbose=0,
compact=True,
):
""" Transform ij of (ij|L) to MOs.
"""
assert aosym in ("s1", "s2ij")
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
cholesky_eri_b(mol, swapfile.name, auxbasis, dataname, int3c, aosym, int2c, comp, ioblk_size, verbose=log)
fswap = h5py.File(swapfile.name, "r")
time1 = log.timer("AO->MO eri transformation 1 pass", *time0)
nmoi = mo_coeffs[0].shape[1]
nmoj = mo_coeffs[1].shape[1]
nao = mo_coeffs[0].shape[0]
auxmol = incore.format_aux_basis(mol, auxbasis)
naoaux = auxmol.nao_nr()
aosym = _stand_sym_code(aosym)
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")
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del (feri[dataname])
else:
feri = h5py.File(erifile, "w")
if comp == 1:
chunks = (min(int(64e3 / nmoj), naoaux), nmoj) # 512K
h5d_eri = feri.create_dataset(dataname, (naoaux, nij_pair), "f8", chunks=chunks)
else:
chunks = (1, min(int(64e3 / nmoj), naoaux), nmoj) # 512K
h5d_eri = feri.create_dataset(dataname, (comp, naoaux, nij_pair), "f8", chunks=chunks)
aopairblks = len(fswap[dataname + "/0"])
iolen = min(int(ioblk_size * 1e6 / 8 / (nao_pair + nij_pair)), naoaux)
totstep = (naoaux + iolen - 1) // iolen * comp
buf = numpy.empty((iolen, nao_pair))
ti0 = time1
for icomp in range(comp):
istep = 0
for row0, row1 in prange(0, naoaux, iolen):
nrow = row1 - row0
istep += 1
log.debug("step 2 [%d/%d], [%d,%d:%d], row = %d", istep, totstep, icomp, row0, row1, nrow)
col0 = 0
for ic in range(aopairblks):
dat = fswap["%s/%d/%d" % (dataname, icomp, ic)]
col1 = col0 + dat.shape[1]
buf[:nrow, col0:col1] = dat[row0:row1]
col0 = col1
buf1 = _ao2mo.nr_e2(buf[:nrow], moij, ijshape, aosym_as_nr_e2, ijmosym)
if comp == 1:
h5d_eri[row0:row1] = buf1
else:
h5d_eri[icomp, row0:row1] = buf1
ti0 = log.timer("step 2 [%d/%d], [%d,%d:%d], row = %d" % (istep, totstep, icomp, 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='eri_mo', tmpdir=None,
int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph', comp=1,
ioblk_size=256, verbose=0):
'''3-center 2-electron AO integrals
'''
assert(aosym in ('s1', 's2ij'))
assert(comp == 1)
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
cholesky_eri_b(mol, swapfile.name, auxbasis, dataname,
int3c, aosym, int2c, comp, ioblk_size, verbose=log)
fswap = h5py.File(swapfile.name, 'r')
time1 = log.timer('generate (ij|L) 1 pass', *time0)
nao = mol.nao_nr()
auxmol = incore.format_aux_basis(mol, auxbasis)
naoaux = auxmol.nao_nr()
aosym = _stand_sym_code(aosym)
if aosym == 's1':
nao_pair = nao * nao
else:
nao_pair = nao * (nao+1) // 2
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
if comp == 1:
chunks = (min(int(16e3/nao),naoaux), nao) # 128K
h5d_eri = feri.create_dataset(dataname, (naoaux,nao_pair), 'f8',
chunks=chunks)
aopairblks = len(fswap[dataname])
else:
chunks = (1, min(int(16e3/nao),naoaux), nao) # 128K
h5d_eri = feri.create_dataset(dataname, (comp,naoaux,nao_pair), 'f8',
chunks=chunks)
aopairblks = len(fswap[dataname+'/0'])
if comp > 1:
for icomp in range(comp):
feri.create_group(str(icomp)) # for h5py old version
iolen = min(int(ioblk_size*1e6/8/nao_pair), naoaux)
totstep = (naoaux+iolen-1)//iolen * comp
buf = numpy.empty((iolen, nao_pair))
istep = 0
ti0 = time1
for icomp in range(comp):
for row0, row1 in prange(0, naoaux, iolen):
nrow = row1 - row0
istep += 1
col0 = 0
for ic in range(aopairblks):
if comp == 1:
dat = fswap['%s/%d'%(dataname,ic)]
else:
dat = fswap['%s/%d/%d'%(dataname,icomp,ic)]
col1 = col0 + dat.shape[1]
buf[:nrow,col0:col1] = dat[row0:row1]
col0 = col1
if comp == 1:
h5d_eri[row0:row1] = buf[:nrow]
else:
h5d_eri[icomp,row0:row1] = buf[:nrow]
ti0 = log.timer('step 2 [%d/%d], [%d,%d:%d], row = %d'%
(istep, totstep, icomp, row0, row1, nrow), *ti0)
fswap.close()
feri.close()
log.timer('cholesky_eri', *time0)
return erifile
def general(mol, mo_coeffs, erifile, auxbasis='weigend+etb', dataname='eri_mo', tmpdir=None,
int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph', comp=1,
max_memory=2000, ioblk_size=256, verbose=0, compact=True):
''' Transform ij of (ij|L) to MOs.
'''
assert(aosym in ('s1', 's2ij'))
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
cholesky_eri_b(mol, swapfile.name, auxbasis, dataname,
int3c, aosym, int2c, comp, ioblk_size, verbose=log)
fswap = h5py.File(swapfile.name, 'r')
time1 = log.timer('AO->MO eri transformation 1 pass', *time0)
nmoi = mo_coeffs[0].shape[1]
nmoj = mo_coeffs[1].shape[1]
nao = mo_coeffs[0].shape[0]
auxmol = incore.format_aux_basis(mol, auxbasis)
naoaux = auxmol.nao_nr()
aosym = _stand_sym_code(aosym)
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')
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
if comp == 1:
chunks = (min(int(16e3/nmoj),naoaux), nmoj) # 128K
h5d_eri = feri.create_dataset(dataname, (naoaux,nij_pair), 'f8',
chunks=chunks)
else:
chunks = (1, min(int(16e3/nmoj),naoaux), nmoj) # 128K
h5d_eri = feri.create_dataset(dataname, (comp,naoaux,nij_pair), 'f8',
chunks=chunks)
aopairblks = len(fswap[dataname+'/0'])
iolen = min(int(ioblk_size*1e6/8/(nao_pair+nij_pair)), naoaux)
totstep = (naoaux+iolen-1)//iolen * comp
buf = numpy.empty((iolen, nao_pair))
ti0 = time1
for icomp in range(comp):
istep = 0
for row0, row1 in prange(0, naoaux, iolen):
nrow = row1 - row0
istep += 1
log.debug('step 2 [%d/%d], [%d,%d:%d], row = %d',
istep, totstep, icomp, row0, row1, nrow)
col0 = 0
for ic in range(aopairblks):
dat = fswap['%s/%d/%d'%(dataname,icomp,ic)]
col1 = col0 + dat.shape[1]
buf[:nrow,col0:col1] = dat[row0:row1]
col0 = col1
buf1 = _ao2mo.nr_e2(buf[:nrow], moij, ijshape, aosym_as_nr_e2, ijmosym)
if comp == 1:
h5d_eri[row0:row1] = buf1
else:
h5d_eri[icomp,row0:row1] = buf1
ti0 = log.timer('step 2 [%d/%d], [%d,%d:%d], row = %d'%
(istep, totstep, icomp, 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_b(mol, erifile, auxbasis='weigend+etb', dataname='eri_mo',
int3c='int3c2e_sph', aosym='s2ij', int2c='int2c2e_sph',
comp=1, ioblk_size=256, auxmol=None, verbose=logger.NOTE):
'''3-center 2-electron AO integrals
'''
assert(aosym in ('s1', 's2ij'))
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
if auxmol is None:
auxmol = format_aux_basis(mol, auxbasis)
j2c = auxmol.intor(int2c, hermi=1)
log.debug('size of aux basis %d', j2c.shape[0])
time1 = log.timer('2c2e', *time0)
try:
low = scipy.linalg.cholesky(j2c, lower=True)
except scipy.linalg.LinAlgError:
j2c[numpy.diag_indices(j2c.shape[1])] += 1e-14
low = scipy.linalg.cholesky(j2c, lower=True)
j2c = None
naux = low.shape[0]
time1 = log.timer('Cholesky 2c2e', *time1)
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
for icomp in range(comp):
feri.create_group('%s/%d'%(dataname,icomp)) # for h5py old version
def store(b, label):
if b.ndim == 3 and b.flags.f_contiguous:
b = lib.transpose(b.T, axes=(0,2,1)).reshape(naux,-1)
else:
b = b.reshape((-1,naux)).T
cderi = scipy.linalg.solve_triangular(low, b, lower=True, overwrite_b=True)
feri[label] = cderi
int3c = gto.moleintor.ascint3(int3c)
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
ao_loc = gto.moleintor.make_loc(bas, int3c)
nao = ao_loc[mol.nbas]
naoaux = ao_loc[-1] - nao
if aosym == 's1':
nao_pair = nao * nao
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's1')
else:
nao_pair = nao * (nao+1) // 2
buflen = min(max(int(ioblk_size*1e6/8/naoaux/comp), 1), nao_pair)
shranges = _guess_shell_ranges(mol, buflen, 's2ij')
log.debug('erifile %.8g MB, IO buf size %.8g MB',
naoaux*nao_pair*8/1e6, comp*buflen*naoaux*8/1e6)
if log.verbose >= logger.DEBUG1:
log.debug1('shranges = %s', shranges)
cintopt = gto.moleintor.make_cintopt(atm, bas, env, int3c)
bufs1 = numpy.empty((comp*max([x[2] for x in shranges]),naoaux))
for istep, sh_range in enumerate(shranges):
log.debug('int3c2e [%d/%d], AO [%d:%d], nrow = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, nrow = sh_range
shls_slice = (bstart, bend, 0, mol.nbas, mol.nbas, mol.nbas+auxmol.nbas)
buf = gto.moleintor.getints3c(int3c, atm, bas, env, shls_slice, comp,
aosym, ao_loc, cintopt, out=bufs1)
if comp == 1:
store(buf, '%s/0/%d'%(dataname,istep))
else:
for icomp in range(comp):
store(buf[icomp], '%s/%d/%d'%(dataname,icomp,istep))
time1 = log.timer('gen CD eri [%d/%d]' % (istep+1,len(shranges)), *time1)
buf = bufs1 = None
feri.close()
return erifile
