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 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 _make_Lpq(mydf, mol, auxmol):
atm, bas, env, ao_loc = incore._env_and_aoloc('cint3c1e_sph', mol, auxmol)
nao = ao_loc[mol.nbas]
naux = ao_loc[-1] - nao
nao_pair = nao * (nao+1) // 2
if mydf.metric.upper() == 'S':
intor = 'cint3c1e_sph'
s_aux = auxmol.intor_symmetric('cint1e_ovlp_sph')
elif mydf.metric.upper() == 'T':
intor = 'cint3c1e_p2_sph'
s_aux = auxmol.intor_symmetric('cint1e_kin_sph') * 2
else: # metric.upper() == 'J'
intor = 'cint3c2e_sph'
s_aux = incore.fill_2c2e(mol, auxmol)
cintopt = gto.moleintor.make_cintopt(atm, bas, env, intor)
if mydf.charge_constraint:
ovlp = lib.pack_tril(mol.intor_symmetric('cint1e_ovlp_sph'))
aux_loc = auxmol.ao_loc_nr()
s_index = numpy.hstack([range(aux_loc[i],aux_loc[i+1])
for i,l in enumerate(auxmol._bas[:,ANG_OF]) if l == 0])
a = numpy.zeros((naux+1,naux+1))
a[:naux,:naux] = s_aux
a[naux,s_index] = a[s_index,naux] = 1
try:
cd = scipy.linalg.cho_factor(a)
def solve(Lpq):
return scipy.linalg.cho_solve(cd, Lpq)
except scipy.linalg.LinAlgError:
def solve(Lpq):
return scipy.linalg.solve(a, Lpq)
else:
cd = scipy.linalg.cho_factor(s_aux)
def solve(Lpq):
return scipy.linalg.cho_solve(cd, Lpq, overwrite_b=True)
def get_Lpq(shls_slice, col0, col1, buf):
# Be cautious here, _ri.nr_auxe2 assumes buf in F-order
Lpq = _ri.nr_auxe2(intor, atm, bas, env, shls_slice, ao_loc,
's2ij', 1, cintopt, buf).T
if mydf.charge_constraint:
Lpq = numpy.ndarray(shape=(naux+1,col1-col0), buffer=buf)
Lpq[naux,:] = ovlp[col0:col1]
Lpq1 = solve(Lpq)
assert(Lpq1.flags.f_contiguous)
lib.transpose(Lpq1.T, out=Lpq)
return Lpq[:naux]
else:
return solve(Lpq)
return get_Lpq
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_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