def test_aux_e2_diff_bra_ket(self):
mol1 = mol.copy()
mol1.basis = 'sto3g'
mol1.build(0, 0, verbose=0)
atm1, bas1, env1 = gto.conc_env(atm, bas, env,
mol1._atm, mol1._bas, mol1._env)
ao_loc = gto.moleintor.make_loc(bas1, 'cint3c2e_sph')
shls_slice = (0, mol.nbas,
mol.nbas+auxmol.nbas, mol.nbas+auxmol.nbas+mol1.nbas,
mol.nbas, mol.nbas+auxmol.nbas)
j3c = _ri.nr_auxe2('cint3c2e_sph', atm1, bas1, env1, shls_slice,
ao_loc, 's1', 1)
nao = mol.nao_nr()
naoj = mol1.nao_nr()
naoaux = auxmol.nao_nr()
eri0 = numpy.empty((nao,naoj,naoaux))
pi = 0
for i in range(mol.nbas):
pj = 0
for j in range(mol.nbas+auxmol.nbas, len(bas1)):
pk = 0
for k in range(mol.nbas, mol.nbas+auxmol.nbas):
shls = (i, j, k)
buf = gto.moleintor.getints_by_shell('cint3c2e_sph',
shls, atm1, bas1, env1)
di, dj, dk = buf.shape
eri0[pi:pi+di,pj:pj+dj,pk:pk+dk] = buf
pk += dk
pj += dj
pi += di
self.assertTrue(numpy.allclose(eri0.reshape(-1,naoaux), j3c))
def aux_e2(mol, auxmol, intor='cint3c2e_sph', aosym='s1', comp=1, out=None):
'''3-center AO integrals (ij|L), where L is the auxiliary basis.
'''
atm, bas, env, ao_loc = _env_and_aoloc(intor, mol, auxmol)
shls_slice = (0, mol.nbas, 0, mol.nbas, mol.nbas, mol.nbas+auxmol.nbas)
return _ri.nr_auxe2(intor, atm, bas, env, shls_slice, ao_loc,
aosym, comp, out=out)
def test_aux_e2_diff_bra_ket(self):
mol1 = mol.copy()
mol1.basis = 'sto3g'
mol1.build(0, 0, verbose=0)
atm1, bas1, env1 = gto.conc_env(atm, bas, env, mol1._atm, mol1._bas,
mol1._env)
ao_loc = gto.moleintor.make_loc(bas1, 'cint3c2e_sph')
shls_slice = (0, mol.nbas, mol.nbas + auxmol.nbas,
mol.nbas + auxmol.nbas + mol1.nbas, mol.nbas,
mol.nbas + auxmol.nbas)
j3c = _ri.nr_auxe2('cint3c2e_sph', atm1, bas1, env1, shls_slice,
ao_loc, 's1', 1)
nao = mol.nao_nr()
naoj = mol1.nao_nr()
naoaux = auxmol.nao_nr()
eri0 = numpy.empty((nao, naoj, naoaux))
pi = 0
for i in range(mol.nbas):
pj = 0
for j in range(mol.nbas + auxmol.nbas, len(bas1)):
pk = 0
for k in range(mol.nbas, mol.nbas + auxmol.nbas):
shls = (i, j, k)
buf = gto.moleintor.getints_by_shell(
'cint3c2e_sph', shls, atm1, bas1, env1)
di, dj, dk = buf.shape
eri0[pi:pi + di, pj:pj + dj, pk:pk + dk] = buf
pk += dk
pj += dj
pi += di
self.assertTrue(numpy.allclose(eri0.reshape(-1, naoaux), j3c))
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)
def aux_e2(mol, auxmol, intor='cint3c2e_sph', aosym='s1', comp=1, out=None):
'''3-center AO integrals (ij|L), where L is the auxiliary basis.
'''
atm, bas, env, ao_loc = _env_and_aoloc(intor, mol, auxmol)
shls_slice = (0, mol.nbas, 0, mol.nbas, mol.nbas, mol.nbas + auxmol.nbas)
return _ri.nr_auxe2(intor,
atm,
bas,
env,
shls_slice,
ao_loc,
aosym,
comp,
out=out)
def aux_e2(mol, auxmol, intor="cint3c2e_sph", aosym="s1", comp=1, hermi=0, mol1=None):
"""3-center AO integrals (ij|L), where L is the auxiliary basis.
"""
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env, auxmol._atm, auxmol._bas, auxmol._env)
if "cart" in intor:
iloc = jloc = _ri.make_loc(0, mol.nbas, _ri._cgto_cart(bas))
else:
iloc = jloc = _ri.make_loc(0, mol.nbas, _ri._cgto_spheric(bas))
if mol1 is None:
basrange = (0, mol.nbas, 0, mol.nbas, mol.nbas, auxmol.nbas)
else:
# Append mol1 next to auxmol
atm, bas, env = gto.mole.conc_env(atm, bas, env, mol1._atm, mol1._bas, mol1._env)
basrange = (0, mol.nbas, mol.nbas + auxmol.nbas, mol1.nbas, mol.nbas, auxmol.nbas)
jloc = None
eri = _ri.nr_auxe2(intor, basrange, atm, bas, env, aosym, comp, iloc=iloc, jloc=jloc)
return eri
def aux_e2(mol, auxmol, intor='cint3c2e_sph', aosym='s1', comp=1, hermi=0,
mol1=None):
'''3-center AO integrals (ij|L), where L is the auxiliary basis.
'''
atm, bas, env = gto.mole.conc_env(mol._atm, mol._bas, mol._env,
auxmol._atm, auxmol._bas, auxmol._env)
if 'cart' in intor:
iloc = jloc = _ri.make_loc(0, mol.nbas, bas, True)
else:
iloc = jloc = _ri.make_loc(0, mol.nbas, bas)
if mol1 is None:
basrange = (0, mol.nbas, 0, mol.nbas, mol.nbas, auxmol.nbas)
else:
# Append mol1 next to auxmol
atm, bas, env = gto.mole.conc_env(atm, bas, env,
mol1._atm, mol1._bas, mol1._env)
basrange = (0, mol.nbas, mol.nbas+auxmol.nbas, mol1.nbas,
mol.nbas, auxmol.nbas)
jloc = _ri.make_loc(0, mol1.nbas, mol1._bas)
eri = _ri.nr_auxe2(intor, basrange,
atm, bas, env, aosym, comp, iloc=iloc, jloc=jloc)
return eri
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 _make_j3c(mydf, mol, auxmol):
log = logger.Logger(mydf.stdout, mydf.verbose)
atm, bas, env, ao_loc = incore._env_and_aoloc('cint3c2e_sph', mol, auxmol)
nao = ao_loc[mol.nbas]
naux = ao_loc[-1] - nao
nao_pair = nao * (nao+1) // 2
cintopt = gto.moleintor.make_cintopt(atm, bas, env, 'cint3c2e_sph')
if mydf.approx_sr_level == 0:
get_Lpq = _make_Lpq(mydf, mol, auxmol)
else:
get_Lpq = _make_Lpq_atomic_approx(mydf, mol, auxmol)
feri = h5py.File(mydf._cderi)
chunks = (min(256,naux), min(256,nao_pair)) # 512K
feri.create_dataset('j3c', (naux,nao_pair), 'f8', chunks=chunks)
feri.create_dataset('Lpq', (naux,nao_pair), 'f8', chunks=chunks)
def save(label, dat, col0, col1):
feri[label][:,col0:col1] = dat
Gv, Gvbase, kws = non_uniform_kgrids(mydf.gs)
nxyz = [i*2 for i in mydf.gs]
gxyz = lib.cartesian_prod([range(i) for i in nxyz])
kk = numpy.einsum('ki,ki->k', Gv, Gv)
idx = numpy.argsort(kk)[::-1]
kk = kk[idx]
Gv = Gv[idx]
kws = kws[idx]
gxyz = gxyz[idx]
coulG = .5/numpy.pi**2 * kws / kk
aoaux = ft_ao.ft_ao(auxmol, Gv, None, Gvbase, gxyz, nxyz)
kLR = numpy.asarray(aoaux.real, order='C')
kLI = numpy.asarray(aoaux.imag, order='C')
j2c = auxmol.intor('cint2c2e_sph', hermi=1).T # .T to C-ordr
lib.dot(kLR.T*coulG, kLR, -1, j2c, 1)
lib.dot(kLI.T*coulG, kLI, -1, j2c, 1)
kLR *= coulG.reshape(-1,1)
kLI *= coulG.reshape(-1,1)
aoaux = coulG = kk = kws = idx = None
max_memory = max(2000, mydf.max_memory-lib.current_memory()[0])
buflen = min(max(int(max_memory*.3*1e6/8/naux), 1), nao_pair)
shranges = outcore._guess_shell_ranges(mol, buflen, 's2ij')
buflen = max([x[2] for x in shranges])
blksize = max(16, int(max_memory*.15*1e6/16/buflen))
pqkbuf = numpy.empty(buflen*blksize)
bufs1 = numpy.empty((buflen*naux))
# bufs2 holds either Lpq and ft_aopair
bufs2 = numpy.empty(max(buflen*(naux+1),buflen*blksize*2)) # *2 for cmplx
col1 = 0
for istep, sh_range in enumerate(shranges):
log.debug('int3c2e [%d/%d], AO [%d:%d], ncol = %d', \
istep+1, len(shranges), *sh_range)
bstart, bend, ncol = sh_range
col0, col1 = col1, col1+ncol
shls_slice = (bstart, bend, 0, bend, mol.nbas, mol.nbas+auxmol.nbas)
Lpq = get_Lpq(shls_slice, col0, col1, bufs2)
save('Lpq', Lpq, col0, col1)
j3c = _ri.nr_auxe2('cint3c2e_sph', atm, bas, env, shls_slice, ao_loc,
's2ij', 1, cintopt, bufs1)
j3c = j3c.T # -> (L|pq) in C-order
lib.dot(j2c, Lpq, -.5, j3c, 1)
Lpq = None
for p0, p1 in lib.prange(0, Gv.shape[0], blksize):
aoao = ft_ao.ft_aopair(mol, Gv[p0:p1], shls_slice[:4], 's2',
Gvbase, gxyz[p0:p1], nxyz, buf=bufs2)
nG = p1 - p0
pqkR = numpy.ndarray((ncol,nG), buffer=pqkbuf)
pqkR[:] = aoao.real.T
lib.dot(kLR[p0:p1].T, pqkR.T, -1, j3c, 1)
pqkI = numpy.ndarray((ncol,nG), buffer=pqkbuf)
pqkI[:] = aoao.imag.T
lib.dot(kLI[p0:p1].T, pqkI.T, -1, j3c, 1)
aoao = aoaux = None
save('j3c', j3c, col0, col1)
feri.close()
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
