def half_e1(mol, mo_coeffs, swapfile,
intor='int2e_spinor', aosym='s4', comp=None,
max_memory=MAX_MEMORY, ioblk_size=IOBLK_SIZE, verbose=logger.WARN,
ao2mopt=None):
time0 = (time.clock(), time.time())
log = logger.new_logger(mol, verbose)
ijsame = 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]
aosym = outcore._stand_sym_code(aosym)
if aosym in ('s1', 's2kl', 'a2kl'):
nao_pair = nao * nao
else:
nao_pair = _count_naopair(mol, nao)
nij_pair = nmoi * nmoj
if ijsame and aosym in ('s4', 's2ij', 'a2ij', 'a4ij', 'a4kl', 'a4'):
log.debug('i-mo == j-mo')
moij = numpy.asarray(mo_coeffs[0], order='F')
ijshape = (0, nmoi, 0, nmoi)
else:
moij = numpy.asarray(numpy.hstack((mo_coeffs[0],mo_coeffs[1])), order='F')
ijshape = (0, nmoi, nmoi, nmoi+nmoj)
e1buflen, mem_words, iobuf_words, ioblk_words = \
guess_e1bufsize(max_memory, ioblk_size, nij_pair, nao_pair, comp)
# The buffer to hold AO integrals in C code
aobuflen = int((mem_words - iobuf_words) // (nao*nao*comp))
shranges = outcore.guess_shell_ranges(mol, (aosym not in ('s1', 's2ij', 'a2ij')),
aobuflen, e1buflen, mol.ao_loc_2c(), False)
if ao2mopt is None:
# if intor == 'int2e_spinor':
# ao2mopt = _ao2mo.AO2MOpt(mol, intor, 'CVHFnr_schwarz_cond',
# 'CVHFsetnr_direct_scf')
# elif intor == 'int2e_spsp1_spinor':
# elif intor == 'int2e_spsp1spsp2_spinor':
# else:
# ao2mopt = _ao2mo.AO2MOpt(mol, intor)
ao2mopt = _ao2mo.AO2MOpt(mol, intor)
log.debug('step1: tmpfile %.8g MB', nij_pair*nao_pair*16/1e6)
log.debug('step1: (ij,kl) = (%d,%d), mem cache %.8g MB, iobuf %.8g MB',
nij_pair, nao_pair, mem_words*16/1e6, iobuf_words*16/1e6)
fswap = h5py.File(swapfile, 'w')
for icomp in range(comp):
g = fswap.create_group(str(icomp)) # for h5py old version
tao = numpy.asarray(mol.tmap(), dtype=numpy.int32)
# transform e1
ti0 = log.timer('Initializing ao2mo.outcore.half_e1', *time0)
nstep = len(shranges)
for istep,sh_range in enumerate(shranges):
log.debug('step 1 [%d/%d], AO [%d:%d], len(buf) = %d', \
istep+1, nstep, *(sh_range[:3]))
buflen = sh_range[2]
iobuf = numpy.empty((comp,buflen,nij_pair), dtype=numpy.complex)
nmic = len(sh_range[3])
p0 = 0
for imic, aoshs in enumerate(sh_range[3]):
log.debug1(' fill iobuf micro [%d/%d], AO [%d:%d], len(aobuf) = %d', \
imic+1, nmic, *aoshs)
buf = _ao2mo.r_e1(intor, moij, ijshape, aoshs,
mol._atm, mol._bas, mol._env,
tao, aosym, comp, ao2mopt)
iobuf[:,p0:p0+aoshs[2]] = buf
p0 += aoshs[2]
ti2 = log.timer('gen AO/transform MO [%d/%d]'%(istep+1,nstep), *ti0)
e2buflen, chunks = guess_e2bufsize(ioblk_size, nij_pair, buflen)
for icomp in range(comp):
dset = fswap.create_dataset('%d/%d'%(icomp,istep),
(nij_pair,iobuf.shape[1]), 'c16',
chunks=None)
for col0, col1 in prange(0, nij_pair, e2buflen):
dset[col0:col1] = lib.transpose(iobuf[icomp,:,col0:col1])
ti0 = log.timer('transposing to disk', *ti2)
fswap.close()
return swapfile
def half_e1(mol, mo_coeffs, swapfile,
intor='cint2e', aosym='s4', comp=1,
max_memory=4000, ioblk_size=256, verbose=logger.WARN, ao2mopt=None):
time0 = (time.clock(), time.time())
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
ijsame = 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]
aosym = _stand_sym_code(aosym)
if aosym in ('s1', 's2kl', 'a2kl'):
nao_pair = nao * nao
else:
nao_pair = guess_nao_pair(mol, nao)
nij_pair = nmoi * nmoj
if ijsame and aosym in ('s4', 's2ij', 'a2ij', 'a4ij', 'a4kl', 'a4'):
log.debug('i-mo == j-mo')
moij = numpy.asarray(mo_coeffs[0], order='F')
ijshape = (0, nmoi, 0, nmoi)
else:
moij = numpy.asarray(numpy.hstack((mo_coeffs[0],mo_coeffs[1])), order='F')
ijshape = (0, nmoi, nmoi, nmoi+nmoj)
e1buflen, mem_words, iobuf_words, ioblk_words = \
guess_e1bufsize(max_memory, ioblk_size, nij_pair, nao_pair, comp)
# The buffer to hold AO integrals in C code
aobuflen = int((mem_words - iobuf_words) // (nao*nao*comp))
shranges = outcore.guess_shell_ranges(mol, (aosym not in ('s1', 's2kl', 'a2kl')),
aobuflen, e1buflen, mol.ao_loc_2c(), False)
if ao2mopt is None:
# if intor == 'cint2e':
# ao2mopt = _ao2mo.AO2MOpt(mol, intor, 'CVHFnr_schwarz_cond',
# 'CVHFsetnr_direct_scf')
# elif intor == 'cint2e_spsp1':
# elif intor == 'cint2e_spsp1spsp2':
# else:
# ao2mopt = _ao2mo.AO2MOpt(mol, intor)
ao2mopt = _ao2mo.AO2MOpt(mol, intor)
log.debug('step1: tmpfile %.8g MB', nij_pair*nao_pair*16/1e6)
log.debug('step1: (ij,kl) = (%d,%d), mem cache %.8g MB, iobuf %.8g MB',
nij_pair, nao_pair, mem_words*16/1e6, iobuf_words*16/1e6)
fswap = h5py.File(swapfile, 'w')
for icomp in range(comp):
g = fswap.create_group(str(icomp)) # for h5py old version
tao = numpy.asarray(mol.tmap(), dtype=numpy.int32)
# transform e1
ti0 = log.timer('Initializing ao2mo.outcore.half_e1', *time0)
nstep = len(shranges)
for istep,sh_range in enumerate(shranges):
log.debug('step 1 [%d/%d], AO [%d:%d], len(buf) = %d', \
istep+1, nstep, *(sh_range[:3]))
buflen = sh_range[2]
iobuf = numpy.empty((comp,buflen,nij_pair), dtype=numpy.complex)
nmic = len(sh_range[3])
p0 = 0
for imic, aoshs in enumerate(sh_range[3]):
log.debug1(' fill iobuf micro [%d/%d], AO [%d:%d], len(aobuf) = %d', \
imic+1, nmic, *aoshs)
buf = _ao2mo.r_e1(intor, moij, ijshape, aoshs,
mol._atm, mol._bas, mol._env,
tao, aosym, comp, ao2mopt)
iobuf[:,p0:p0+aoshs[2]] = buf
p0 += aoshs[2]
ti2 = log.timer('gen AO/transform MO [%d/%d]'%(istep+1,nstep), *ti0)
e2buflen, chunks = guess_e2bufsize(ioblk_size, nij_pair, buflen)
for icomp in range(comp):
dset = fswap.create_dataset('%d/%d'%(icomp,istep),
(nij_pair,iobuf.shape[1]), 'c16',
chunks=None)
for col0, col1 in prange(0, nij_pair, e2buflen):
dset[col0:col1] = pyscf.lib.transpose(iobuf[icomp,:,col0:col1])
ti0 = log.timer('transposing to disk', *ti2)
fswap.close()
return swapfile