def general(mol, mo_coeffs, erifile, dataname='eri_mo',
intor='int2e_spinor', aosym='s4', comp=None,
max_memory=MAX_MEMORY, ioblk_size=IOBLK_SIZE, verbose=logger.WARN):
time_0pass = (time.clock(), time.time())
log = logger.new_logger(mol, verbose)
if '_spinor' not in intor:
log.warn('r_ao2mo requires spinor integrals.\n'
'Suffix _spinor is added to %s', intor)
intor = intor + '_spinor'
intor, comp = gto.moleintor._get_intor_and_comp(mol._add_suffix(intor), comp)
klsame = iden_coeffs(mo_coeffs[2], mo_coeffs[3])
nmoi = mo_coeffs[0].shape[1]
nmoj = mo_coeffs[1].shape[1]
nmok = mo_coeffs[2].shape[1]
nmol = mo_coeffs[3].shape[1]
nao = mo_coeffs[0].shape[0]
aosym = outcore._stand_sym_code(aosym)
if aosym in ('s1', 's2ij', 'a2ij'):
nao_pair = nao * nao
else:
nao_pair = _count_naopair(mol, nao)
nij_pair = nmoi*nmoj
nkl_pair = nmok*nmol
if klsame and aosym in ('s4', 's2kl', 'a2kl', 'a4ij', 'a4kl', 'a4'):
log.debug('k-mo == l-mo')
mokl = numpy.asarray(mo_coeffs[2], dtype=numpy.complex128, order='F')
klshape = (0, nmok, 0, nmok)
else:
mokl = numpy.asarray(numpy.hstack((mo_coeffs[2],mo_coeffs[3])),
dtype=numpy.complex128, order='F')
klshape = (0, nmok, nmok, nmok+nmol)
if isinstance(erifile, str):
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile, 'a')
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
else:
assert(isinstance(erifile, h5py.Group))
feri = erifile
if comp == 1:
chunks = (nmoj,nmol)
shape = (nij_pair, nkl_pair)
else:
chunks = (1,nmoj,nmol)
shape = (comp, nij_pair, nkl_pair)
if nij_pair == 0 or nkl_pair == 0:
feri.create_dataset(dataname, shape, 'c16')
if isinstance(erifile, str):
feri.close()
return erifile
else:
h5d_eri = feri.create_dataset(dataname, shape, 'c16', chunks=chunks)
log.debug('MO integrals %s are saved in %s/%s', intor, erifile, dataname)
log.debug('num. MO ints = %.8g, required disk %.8g MB',
float(nij_pair)*nkl_pair*comp, nij_pair*nkl_pair*comp*16/1e6)
# transform e1
swapfile = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
half_e1(mol, mo_coeffs, swapfile.name, intor, aosym, comp,
max_memory, ioblk_size, log)
time_1pass = log.timer('AO->MO transformation for %s 1 pass'%intor,
*time_0pass)
e2buflen = guess_e2bufsize(ioblk_size, nij_pair, nao_pair)[0]
log.debug('step2: kl-pair (ao %d, mo %d), mem %.8g MB, '
'ioblock (r/w) %.8g/%.8g MB', \
nao_pair, nkl_pair, e2buflen*nao_pair*16/1e6,
e2buflen*nij_pair*16/1e6, e2buflen*nkl_pair*16/1e6)
fswap = h5py.File(swapfile.name, 'r')
klaoblks = len(fswap['0'])
ijmoblks = int(numpy.ceil(float(nij_pair)/e2buflen)) * comp
ao_loc = numpy.asarray(mol.ao_loc_2c(), dtype=numpy.int32)
tao = numpy.asarray(mol.tmap(), dtype=numpy.int32)
ti0 = time_1pass
buf = numpy.empty((e2buflen, nao_pair), dtype=numpy.complex)
istep = 0
for row0, row1 in prange(0, nij_pair, e2buflen):
nrow = row1 - row0
for icomp in range(comp):
istep += 1
tioi = 0
log.debug('step 2 [%d/%d], [%d,%d:%d], row = %d', \
istep, ijmoblks, icomp, row0, row1, nrow)
col0 = 0
for ic in range(klaoblks):
dat = fswap['%d/%d'%(icomp,ic)]
col1 = col0 + dat.shape[1]
buf[:nrow,col0:col1] = dat[row0:row1]
col0 = col1
ti2 = log.timer('step 2 [%d/%d], load buf'%(istep,ijmoblks), *ti0)
tioi += ti2[1]-ti0[1]
pbuf = _ao2mo.r_e2(buf[:nrow], mokl, klshape, tao, ao_loc, aosym)
tw1 = time.time()
if comp == 1:
h5d_eri[row0:row1] = pbuf
else:
h5d_eri[icomp,row0:row1] = pbuf
tioi += time.time()-tw1
ti1 = (time.clock(), time.time())
log.debug('step 2 [%d/%d] CPU time: %9.2f, Wall time: %9.2f, I/O time: %9.2f', \
istep, ijmoblks, ti1[0]-ti0[0], ti1[1]-ti0[1], tioi)
ti0 = ti1
buf = pbuf = None
fswap.close()
if isinstance(erifile, str):
feri.close()
log.timer('AO->MO transformation for %s 2 pass'%intor, *time_1pass)
log.timer('AO->MO transformation for %s '%intor, *time_0pass)
return erifile
def general(mol, mo_coeffs, erifile, dataname='eri_mo',
intor='int2e_spinor', aosym='s4', comp=None,
max_memory=MAX_MEMORY, ioblk_size=IOBLK_SIZE, verbose=logger.WARN):
time_0pass = (time.clock(), time.time())
log = logger.new_logger(mol, verbose)
intor, comp = gto.moleintor._get_intor_and_comp(mol._add_suffix(intor), comp)
klsame = iden_coeffs(mo_coeffs[2], mo_coeffs[3])
nmoi = mo_coeffs[0].shape[1]
nmoj = mo_coeffs[1].shape[1]
nmok = mo_coeffs[2].shape[1]
nmol = mo_coeffs[3].shape[1]
nao = mo_coeffs[0].shape[0]
aosym = outcore._stand_sym_code(aosym)
if aosym in ('s1', 's2ij', 'a2ij'):
nao_pair = nao * nao
else:
nao_pair = _count_naopair(mol, nao)
nij_pair = nmoi*nmoj
nkl_pair = nmok*nmol
if klsame and aosym in ('s4', 's2kl', 'a2kl', 'a4ij', 'a4kl', 'a4'):
log.debug('k-mo == l-mo')
mokl = numpy.asarray(mo_coeffs[2], dtype=numpy.complex128, order='F')
klshape = (0, nmok, 0, nmok)
else:
mokl = numpy.asarray(numpy.hstack((mo_coeffs[2],mo_coeffs[3])),
dtype=numpy.complex128, order='F')
klshape = (0, nmok, nmok, nmok+nmol)
if isinstance(erifile, str):
if h5py.is_hdf5(erifile):
feri = h5py.File(erifile)
if dataname in feri:
del(feri[dataname])
else:
feri = h5py.File(erifile, 'w')
else:
assert(isinstance(erifile, h5py.Group))
feri = erifile
if comp == 1:
chunks = (nmoj,nmol)
shape = (nij_pair, nkl_pair)
else:
chunks = (1,nmoj,nmol)
shape = (comp, nij_pair, nkl_pair)
if nij_pair == 0 or nkl_pair == 0:
feri.create_dataset(dataname, shape, 'c16')
if isinstance(erifile, str):
feri.close()
return erifile
else:
h5d_eri = feri.create_dataset(dataname, shape, 'c16', chunks=chunks)
log.debug('MO integrals %s are saved in %s/%s', intor, erifile, dataname)
log.debug('num. MO ints = %.8g, required disk %.8g MB',
float(nij_pair)*nkl_pair*comp, nij_pair*nkl_pair*comp*16/1e6)
# transform e1
swapfile = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
half_e1(mol, mo_coeffs, swapfile.name, intor, aosym, comp,
max_memory, ioblk_size, log)
time_1pass = log.timer('AO->MO transformation for %s 1 pass'%intor,
*time_0pass)
e2buflen = guess_e2bufsize(ioblk_size, nij_pair, nao_pair)[0]
log.debug('step2: kl-pair (ao %d, mo %d), mem %.8g MB, '
'ioblock (r/w) %.8g/%.8g MB', \
nao_pair, nkl_pair, e2buflen*nao_pair*16/1e6,
e2buflen*nij_pair*16/1e6, e2buflen*nkl_pair*16/1e6)
fswap = h5py.File(swapfile.name, 'r')
klaoblks = len(fswap['0'])
ijmoblks = int(numpy.ceil(float(nij_pair)/e2buflen)) * comp
ao_loc = numpy.asarray(mol.ao_loc_2c(), dtype=numpy.int32)
tao = numpy.asarray(mol.tmap(), dtype=numpy.int32)
ti0 = time_1pass
buf = numpy.empty((e2buflen, nao_pair), dtype=numpy.complex)
istep = 0
for row0, row1 in prange(0, nij_pair, e2buflen):
nrow = row1 - row0
for icomp in range(comp):
istep += 1
tioi = 0
log.debug('step 2 [%d/%d], [%d,%d:%d], row = %d', \
istep, ijmoblks, icomp, row0, row1, nrow)
col0 = 0
for ic in range(klaoblks):
dat = fswap['%d/%d'%(icomp,ic)]
col1 = col0 + dat.shape[1]
buf[:nrow,col0:col1] = dat[row0:row1]
col0 = col1
ti2 = log.timer('step 2 [%d/%d], load buf'%(istep,ijmoblks), *ti0)
tioi += ti2[1]-ti0[1]
pbuf = _ao2mo.r_e2(buf[:nrow], mokl, klshape, tao, ao_loc, aosym)
tw1 = time.time()
if comp == 1:
h5d_eri[row0:row1] = pbuf
else:
h5d_eri[icomp,row0:row1] = pbuf
tioi += time.time()-tw1
ti1 = (time.clock(), time.time())
log.debug('step 2 [%d/%d] CPU time: %9.2f, Wall time: %9.2f, I/O time: %9.2f', \
istep, ijmoblks, ti1[0]-ti0[0], ti1[1]-ti0[1], tioi)
ti0 = ti1
buf = pbuf = None
fswap.close()
if isinstance(erifile, str):
feri.close()
log.timer('AO->MO transformation for %s 2 pass'%intor, *time_1pass)
log.timer('AO->MO transformation for %s '%intor, *time_0pass)
return erifile
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='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