def ao2mo(mf, mo_coeff, erifile):
n4c, nmo = mo_coeff.shape
n2c = n4c // 2
c = mf.mol.light_speed
ol = mo_coeff[:n2c]
os = mo_coeff[n2c:] * (.5 / c)
def run(mos, intor, dst, bound, blksize):
logger.debug(mf, 'blksize = %d', blksize)
r_outcore.general(mf.mol,
mos,
erifile,
dataname='tmp',
intor=intor,
verbose=mf.verbose)
with h5py.File(erifile) as feri:
for i0, i1 in prange(0, bound, blksize):
logger.debug(mf, 'load %s %d', intor, i0)
buf = feri[dst][i0:i1]
# Add the contribution from 'tmp' to erifile
buf += feri['tmp'][i0:i1]
feri[dst][i0:i1] = buf
buf = None
r_outcore.general(mf.mol, (ol, ol, ol, ol),
erifile,
dataname='ericas',
intor='cint2e',
verbose=mf.verbose)
blksize = max(1, int(512e6 / 16 / (nmo**3))) * nmo
run((os, os, os, os), 'cint2e_spsp1spsp2', 'ericas', nmo * nmo, blksize)
run((os, os, ol, ol), 'cint2e_spsp1', 'ericas', nmo * nmo, blksize)
run((ol, ol, os, os), 'cint2e_spsp2', 'ericas', nmo * nmo, blksize)
return 0
def no_pair_ovov(mol, mo_coeff, erifile):
'''
2-electron integrals ( o v | o v ) for no-pair Hamiltonian under RKB basis
'''
c = lib.param.LIGHT_SPEED
n4c, nmo = mo_coeff.shape
n2c = n4c // 2
nNeg = nmo // 2
nocc = mol.nelectron
nvir = nmo // 2 - nocc
mo_pos_l = mo_coeff[:n2c,nNeg:]
mo_pos_s = mo_coeff[n2c:,nNeg:] * (.5/c)
Lo = mo_pos_l[:,:nocc]
So = mo_pos_s[:,:nocc]
Lv = mo_pos_l[:,nocc:]
Sv = mo_pos_s[:,nocc:]
dataname = 'dhf_ovov'
def run(mos, intor):
r_outcore.general(mol, mos, erifile,
dataname='tmp', intor=intor)
blksize = 400
nij = mos[0].shape[1] * mos[1].shape[1]
with h5py.File(erifile) as feri:
for i0, i1 in lib.prange(0, nij, blksize):
buf = feri[dataname][i0:i1]
buf += feri['tmp'][i0:i1]
feri[dataname][i0:i1] = buf
r_outcore.general(mol, (Lo, Lv, Lo, Lv), erifile,
dataname=dataname, intor='int2e_spinor')
run((So, Sv, So, Sv), 'int2e_spsp1spsp2_spinor')
run((So, Sv, Lo, Lv), 'int2e_spsp1_spinor' )
run((Lo, Lv, So, Sv), 'int2e_spsp2_spinor' )
def ao2mo(mf, mo_coeff, erifile):
n4c, nmo = mo_coeff.shape
n2c = n4c // 2
nN = nmo // 2
nocc = int(mf.mo_occ.sum())
nP = nN + nocc
nvir = nmo - nP
c = lib.param.LIGHT_SPEED
ol = mo_coeff[:n2c]
os = mo_coeff[n2c:] * (.5 / c)
ol0 = ol[:, nN:nP]
os0 = os[:, nN:nP]
ol1 = ol[:, :nP]
os1 = os[:, :nP]
ol2 = ol[:, nP:]
os2 = os[:, nP:]
ol3 = ol[:, :nN]
os3 = os[:, :nN]
ol4 = ol[:, nN:]
os4 = os[:, nN:]
def run(mos, intor, dst, bound, blksize):
logger.debug(mf, 'blksize = %d', blksize)
r_outcore.general(mf.mol,
mos,
erifile,
dataname='tmp',
intor=intor,
verbose=mf.verbose)
with h5py.File(erifile) as feri:
for i0, i1 in prange(0, bound, blksize):
logger.debug(mf, 'load %s %d', intor, i0)
buf = feri[dst][i0:i1]
buf += feri['tmp'][i0:i1]
feri[dst][i0:i1] = buf
buf = None
r_outcore.general(mf.mol, (ol0, ol2, ol1, ol2),
erifile,
dataname='ij',
intor='cint2e',
verbose=mf.verbose)
blksize = max(1, int(512e6 / 16 / (nvir * nP * nvir))) * nvir
run((os0, os2, os1, os2), 'cint2e_spsp1spsp2', 'ij', nocc * nvir, blksize)
run((os0, os2, ol1, ol2), 'cint2e_spsp1', 'ij', nocc * nvir,
blksize) #ssll
run((ol0, ol2, os1, os2), 'cint2e_spsp2', 'ij', nocc * nvir, blksize)
r_outcore.general(mf.mol, (ol0, ol3, ol4, ol3),
erifile,
dataname='ia',
intor='cint2e',
verbose=mf.verbose)
blksize = max(1, int(512e6 / 16 / (nN * nN * nN))) * nN
run((os0, os3, os4, os3), 'cint2e_spsp1spsp2', 'ia', nocc * nN, blksize)
run((os0, os3, ol4, ol3), 'cint2e_spsp1', 'ia', nocc * nN, blksize)
run((ol0, ol3, os4, os3), 'cint2e_spsp2', 'ia', nocc * nN, blksize)
def run(mos, intor):
r_outcore.general(mol, mos, erifile,
dataname='tmp', intor=intor)
blksize = 400
nij = mos[0].shape[1] * mos[1].shape[1]
with h5py.File(erifile) as feri:
for i0, i1 in lib.prange(0, nij, blksize):
buf = feri[dataname][i0:i1]
buf += feri['tmp'][i0:i1]
feri[dataname][i0:i1] = buf
def run(mos, intor, dst, bound, blksize):
logger.debug(mf, 'blksize = %d', blksize)
r_outcore.general(mf.mol,
mos,
erifile,
dataname='tmp',
intor=intor,
verbose=mf.verbose)
with h5py.File(erifile) as feri:
for i0, i1 in prange(0, bound, blksize):
logger.debug(mf, 'load %s %d', intor, i0)
buf = feri[dst][i0:i1]
buf += feri['tmp'][i0:i1]
feri[dst][i0:i1] = buf
buf = None
'''
MO integral transformation for spinor integrals
'''
import h5py
from pyscf import gto
from pyscf import scf
from pyscf import lib
from pyscf.ao2mo import r_outcore
mol = gto.M(
atom = '''
O 0. 0. 0.
H 0. -0.757 0.587
H 0. 0.757 0.587
''',
basis = 'sto3g',
)
mf = scf.DHF(mol).run()
n4c, nmo = mf.mo_coeff.shape
n2c = n4c // 2
nNeg = nmo // 2
mo = mf.mo_coeff[:n2c,nNeg:]
r_outcore.general(mol, (mo, mo, mo, mo), 'llll.h5', intor='int2e_spinor')
with h5py.File('llll.h5', 'r') as f:
print('Number of DHF molecular orbitals %s' % (nmo//2))
print('MO integrals for large component orbitals. Shape = %s'
% str(f['eri_mo'].shape))