nao = mol.nao_nr()
npair = nao*(nao+1)//2
rhf = scf.RHF(mol)
rhf.scf()
print(logger.process_clock())
full(mol, rhf.mo_coeff, 'h2oeri.h5', max_memory=10, ioblk_size=5)
print(logger.process_clock())
eri0 = incore.full(rhf._eri, rhf.mo_coeff)
feri = h5py.File('h2oeri.h5', 'r')
print('full', abs(eri0-feri['eri_mo']).sum())
feri.close()
print(logger.process_clock())
c = rhf.mo_coeff
general(mol, (c,c,c,c), 'h2oeri.h5', max_memory=10, ioblk_size=5)
print(logger.process_clock())
feri = h5py.File('h2oeri.h5', 'r')
print('general', abs(eri0-feri['eri_mo']).sum())
feri.close()
# set ijsame and klsame to False, then check
c = rhf.mo_coeff
n = c.shape[1]
general(mol, (c,c,c,c), 'h2oeri.h5', max_memory=10, ioblk_size=5, compact=False)
feri = h5py.File('h2oeri.h5', 'r')
eri1 = numpy.array(feri['eri_mo']).reshape(n,n,n,n)
eri1 = addons.restore(4, eri1, n)
print('general', abs(eri0-eri1).sum())
def half_e1(eri_ao, mo_coeffs, compact=True):
r'''Given two set of orbitals, half transform the (ij| pair of 8-fold or
4-fold AO integrals (ij|kl)
Args:
eri_ao : ndarray
AO integrals, can be either 8-fold or 4-fold symmetry.
mo_coeffs : list of ndarray
Two sets of orbital coefficients, corresponding to the i, j
indices of (ij|kl)
Kwargs:
compact : bool
When compact is True, the returned MO integrals uses the highest
possible permutation symmetry. If it's False, the function will
abandon any permutation symmetry, and return the "plain" MO
integrals
Returns:
ndarray of transformed MO integrals. The MO integrals may or may not
have the permutation symmetry, depending on the given orbitals, and
the kwargs compact.
Examples:
>>> from pyscf import gto
>>> from pyscf import ao2mo
>>> mol = gto.M(atom='O 0 0 0; H 0 1 0; H 0 0 1', basis='sto3g')
>>> eri = mol.intor('int2e_sph', aosym='s8')
>>> mo1 = numpy.random.random((mol.nao_nr(), 10))
>>> mo2 = numpy.random.random((mol.nao_nr(), 8))
>>> eri1 = ao2mo.incore.half_e1(eri, (mo1,mo2))
>>> eri1 = ao2mo.incore.half_e1(eri, (mo1,mo2))
>>> print(eri1.shape)
(80, 28)
>>> eri1 = ao2mo.incore.half_e1(eri, (mo1,mo2), compact=False)
>>> print(eri1.shape)
(80, 28)
>>> eri1 = ao2mo.incore.half_e1(eri, (mo1,mo1))
>>> print(eri1.shape)
(55, 28)
'''
eri_ao = numpy.asarray(eri_ao, order='C')
nao, nmoi = mo_coeffs[0].shape
nmoj = mo_coeffs[1].shape[1]
nao_pair = nao*(nao+1)//2
ijmosym, nij_pair, moij, ijshape = _conc_mos(mo_coeffs[0], mo_coeffs[1], compact)
ijshape = (ijshape[0], ijshape[1]-ijshape[0],
ijshape[2], ijshape[3]-ijshape[2])
eri1 = numpy.empty((nij_pair,nao_pair))
if nij_pair == 0:
return eri1
if eri_ao.size == nao_pair**2: # 4-fold symmetry
ftrans = _ao2mo.libao2mo.AO2MOtranse1_incore_s4
elif eri_ao.size == nao_pair*(nao_pair+1)//2:
ftrans = _ao2mo.libao2mo.AO2MOtranse1_incore_s8
else:
from pyscf.ao2mo.addons import restore
eri_ao = restore(4, eri_ao, nao)
ftrans = _ao2mo.libao2mo.AO2MOtranse1_incore_s4
if ijmosym == 's2':
fmmm = _ao2mo.libao2mo.AO2MOmmm_nr_s2_s2
elif nmoi <= nmoj:
fmmm = _ao2mo.libao2mo.AO2MOmmm_nr_s2_iltj
else:
fmmm = _ao2mo.libao2mo.AO2MOmmm_nr_s2_igtj
fdrv = getattr(_ao2mo.libao2mo, 'AO2MOnr_e1incore_drv')
bufs = numpy.empty((BLOCK, nij_pair))
for blk0 in range(0, nao_pair, BLOCK):
blk1 = min(blk0+BLOCK, nao_pair)
buf = bufs[:blk1-blk0]
fdrv(ftrans, fmmm,
buf.ctypes.data_as(ctypes.c_void_p),
eri_ao.ctypes.data_as(ctypes.c_void_p),
moij.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(blk0), ctypes.c_int(blk1-blk0),
ctypes.c_int(nao),
ctypes.c_int(ijshape[0]), ctypes.c_int(ijshape[1]),
ctypes.c_int(ijshape[2]), ctypes.c_int(ijshape[3]))
eri1[:,blk0:blk1] = buf.T
return eri1
nao = mol.nao_nr()
npair = nao*(nao+1)//2
rhf = scf.RHF(mol)
rhf.scf()
print(time.clock())
full(mol, rhf.mo_coeff, 'h2oeri.h5', max_memory=10, ioblk_size=5)
print(time.clock())
eri0 = incore.full(rhf._eri, rhf.mo_coeff)
feri = h5py.File('h2oeri.h5', 'r')
print('full', abs(eri0-feri['eri_mo']).sum())
feri.close()
print(time.clock())
c = rhf.mo_coeff
general(mol, (c,c,c,c), 'h2oeri.h5', max_memory=10, ioblk_size=5)
print(time.clock())
feri = h5py.File('h2oeri.h5', 'r')
print('general', abs(eri0-feri['eri_mo']).sum())
feri.close()
# set ijsame and klsame to False, then check
c = rhf.mo_coeff
n = c.shape[1]
general(mol, (c,c,c,c), 'h2oeri.h5', max_memory=10, ioblk_size=5, compact=False)
feri = h5py.File('h2oeri.h5', 'r')
eri1 = numpy.array(feri['eri_mo']).reshape(n,n,n,n)
eri1 = addons.restore(4, eri1, n)
print('general', abs(eri0-eri1).sum())
def half_e1(eri_ao, mo_coeffs, compact=True):
r'''Given two set of orbitals, half transform the (ij| pair of 8-fold or
4-fold AO integrals (ij|kl)
Args:
eri_ao : ndarray
AO integrals, can be either 8-fold or 4-fold symmetry.
mo_coeffs : list of ndarray
Two sets of orbital coefficients, corresponding to the i, j
indices of (ij|kl)
Kwargs:
compact : bool
When compact is True, the returned MO integrals uses the highest
possible permutation symmetry. If it's False, the function will
abandon any permutation symmetry, and return the "plain" MO
integrals
Returns:
ndarray of transformed MO integrals. The MO integrals may or may not
have the permutation symmetry, depending on the given orbitals, and
the kwargs compact.
Examples:
>>> from pyscf import gto
>>> from pyscf import ao2mo
>>> mol = gto.M(atom='O 0 0 0; H 0 1 0; H 0 0 1', basis='sto3g')
>>> eri = mol.intor('int2e_sph', aosym='s8')
>>> mo1 = numpy.random.random((mol.nao_nr(), 10))
>>> mo2 = numpy.random.random((mol.nao_nr(), 8))
>>> eri1 = ao2mo.incore.half_e1(eri, (mo1,mo2))
>>> eri1 = ao2mo.incore.half_e1(eri, (mo1,mo2))
>>> print(eri1.shape)
(80, 28)
>>> eri1 = ao2mo.incore.half_e1(eri, (mo1,mo2), compact=False)
>>> print(eri1.shape)
(80, 28)
>>> eri1 = ao2mo.incore.half_e1(eri, (mo1,mo1))
>>> print(eri1.shape)
(55, 28)
'''
eri_ao = numpy.asarray(eri_ao, order='C')
nao, nmoi = mo_coeffs[0].shape
nmoj = mo_coeffs[1].shape[1]
nao_pair = nao * (nao + 1) // 2
ijmosym, nij_pair, moij, ijshape = _conc_mos(mo_coeffs[0], mo_coeffs[1],
compact)
ijshape = (ijshape[0], ijshape[1] - ijshape[0], ijshape[2],
ijshape[3] - ijshape[2])
eri1 = numpy.empty((nij_pair, nao_pair))
if nij_pair == 0:
return eri1
if eri_ao.size == nao_pair**2: # 4-fold symmetry
ftrans = _ao2mo.libao2mo.AO2MOtranse1_incore_s4
elif eri_ao.size == nao_pair * (nao_pair + 1) // 2:
ftrans = _ao2mo.libao2mo.AO2MOtranse1_incore_s8
else:
from pyscf.ao2mo.addons import restore
eri_ao = restore(4, eri_ao, nao)
ftrans = _ao2mo.libao2mo.AO2MOtranse1_incore_s4
if ijmosym == 's2':
fmmm = _ao2mo.libao2mo.AO2MOmmm_nr_s2_s2
elif nmoi <= nmoj:
fmmm = _ao2mo.libao2mo.AO2MOmmm_nr_s2_iltj
else:
fmmm = _ao2mo.libao2mo.AO2MOmmm_nr_s2_igtj
fdrv = getattr(_ao2mo.libao2mo, 'AO2MOnr_e1incore_drv')
bufs = numpy.empty((BLOCK, nij_pair))
for blk0 in range(0, nao_pair, BLOCK):
blk1 = min(blk0 + BLOCK, nao_pair)
buf = bufs[:blk1 - blk0]
fdrv(ftrans, fmmm, buf.ctypes.data_as(ctypes.c_void_p),
eri_ao.ctypes.data_as(ctypes.c_void_p),
moij.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(blk0),
ctypes.c_int(blk1 - blk0), ctypes.c_int(nao),
ctypes.c_int(ijshape[0]), ctypes.c_int(ijshape[1]),
ctypes.c_int(ijshape[2]), ctypes.c_int(ijshape[3]))
eri1[:, blk0:blk1] = buf.T
return eri1
