def ao2mo(self, mo_coeff=None):
nocc = self.nocc
nvir = self.nmo - nocc
mem_incore, mem_outcore, mem_basic = ccsd._mem_usage(nocc, nvir)
mem_now = lib.current_memory()[0]
if (self._scf._eri is not None and
(mem_incore+mem_now < self.max_memory) or self.mol.incore_anyway):
return _make_eris_incore(self, mo_coeff)
elif hasattr(self._scf, 'with_df'):
raise NotImplementedError
else:
return _make_eris_outcore(self, mo_coeff)
def __init__(self, myci, mo_coeff=None, method='incore'):
cput0 = (time.clock(), time.time())
moidx = numpy.ones(myci.mo_occ.size, dtype=numpy.bool)
if isinstance(myci.frozen, (int, numpy.integer)):
moidx[:myci.frozen] = False
elif len(myci.frozen) > 0:
moidx[numpy.asarray(myci.frozen)] = False
if mo_coeff is None:
self.mo_coeff = mo_coeff = myci.mo_coeff[:, moidx]
else:
self.mo_coeff = mo_coeff = mo_coeff[:, moidx]
dm = myci._scf.make_rdm1(myci.mo_coeff, myci.mo_occ)
fockao = myci._scf.get_hcore() + myci._scf.get_veff(myci.mol, dm)
self.fock = reduce(numpy.dot, (mo_coeff.T, fockao, mo_coeff))
nocc = myci.nocc
nmo = myci.nmo
nvir = nmo - nocc
mem_incore, mem_outcore, mem_basic = ccsd._mem_usage(nocc, nvir)
mem_now = lib.current_memory()[0]
log = logger.Logger(myci.stdout, myci.verbose)
if (method == 'incore' and myci._scf._eri is not None and
(mem_incore + mem_now < myci.max_memory)
or myci.mol.incore_anyway):
eri1 = ao2mo.incore.full(myci._scf._eri, mo_coeff)
#:eri1 = ao2mo.restore(1, eri1, nmo)
#:self.oooo = eri1[:nocc,:nocc,:nocc,:nocc].copy()
#:self.ooov = eri1[:nocc,:nocc,:nocc,nocc:].copy()
#:self.vooo = eri1[nocc:,:nocc,:nocc,:nocc].copy()
#:self.voov = eri1[nocc:,:nocc,:nocc,nocc:].copy()
#:self.vvoo = eri1[nocc:,nocc:,:nocc,:nocc].copy()
#:vovv = eri1[nocc:,:nocc,nocc:,nocc:].copy()
#:self.vovv = lib.pack_tril(vovv.reshape(-1,nvir,nvir))
#:self.vvvv = ao2mo.restore(4, eri1[nocc:,nocc:,nocc:,nocc:], nvir)
nvir_pair = nvir * (nvir + 1) // 2
self.oooo = numpy.empty((nocc, nocc, nocc, nocc))
self.ooov = numpy.empty((nocc, nocc, nocc, nvir))
self.vooo = numpy.empty((nvir, nocc, nocc, nocc))
self.voov = numpy.empty((nvir, nocc, nocc, nvir))
self.vovv = numpy.empty((nvir, nocc, nvir_pair))
self.vvvv = numpy.empty((nvir_pair, nvir_pair))
ij = 0
outbuf = numpy.empty((nmo, nmo, nmo))
oovv = numpy.empty((nocc, nocc, nvir, nvir))
for i in range(nocc):
buf = lib.unpack_tril(eri1[ij:ij + i + 1], out=outbuf[:i + 1])
for j in range(i + 1):
self.oooo[i, j] = self.oooo[j, i] = buf[j, :nocc, :nocc]
self.ooov[i, j] = self.ooov[j, i] = buf[j, :nocc, nocc:]
oovv[i, j] = oovv[j, i] = buf[j, nocc:, nocc:]
ij += i + 1
self.vvoo = lib.transpose(oovv.reshape(nocc**2, -1)).reshape(
nvir, nvir, nocc, nocc)
oovv = None
ij1 = 0
for i in range(nocc, nmo):
buf = lib.unpack_tril(eri1[ij:ij + i + 1], out=outbuf[:i + 1])
self.vooo[i - nocc] = buf[:nocc, :nocc, :nocc]
self.voov[i - nocc] = buf[:nocc, :nocc, nocc:]
lib.pack_tril(_cp(buf[:nocc, nocc:, nocc:]),
out=self.vovv[i - nocc])
dij = i - nocc + 1
lib.pack_tril(_cp(buf[nocc:i + 1, nocc:, nocc:]),
out=self.vvvv[ij1:ij1 + dij])
ij += i + 1
ij1 += dij
else:
cput1 = time.clock(), time.time()
self.feri1 = lib.H5TmpFile()
orbo = mo_coeff[:, :nocc]
orbv = mo_coeff[:, nocc:]
nvpair = nvir * (nvir + 1) // 2
self.oooo = self.feri1.create_dataset('oooo',
(nocc, nocc, nocc, nocc),
'f8')
self.ooov = self.feri1.create_dataset('ooov',
(nocc, nocc, nocc, nvir),
'f8')
self.vvoo = self.feri1.create_dataset('vvoo',
(nvir, nvir, nocc, nocc),
'f8')
self.vooo = self.feri1.create_dataset('vooo',
(nvir, nocc, nocc, nocc),
'f8')
self.voov = self.feri1.create_dataset('voov',
(nvir, nocc, nocc, nvir),
'f8')
self.vovv = self.feri1.create_dataset('vovv', (nvir, nocc, nvpair),
'f8')
fsort = _ccsd.libcc.CCsd_sort_inplace
nocc_pair = nocc * (nocc + 1) // 2
nvir_pair = nvir * (nvir + 1) // 2
def sort_inplace(p0, p1, eri):
fsort(eri.ctypes.data_as(ctypes.c_void_p), ctypes.c_int(nocc),
ctypes.c_int(nvir), ctypes.c_int((p1 - p0) * nocc))
vv = eri[:, :nvir_pair]
oo = eri[:, nvir_pair:nvir_pair + nocc_pair]
ov = eri[:, nvir_pair + nocc_pair:].reshape(-1, nocc, nvir)
return oo, ov, vv
buf = numpy.empty((nmo, nmo, nmo))
oovv = numpy.empty((nocc, nocc, nvir, nvir))
def save_occ_frac(p0, p1, eri):
oo, ov, vv = sort_inplace(p0, p1, eri)
self.oooo[p0:p1] = lib.unpack_tril(oo, out=buf).reshape(
p1 - p0, nocc, nocc, nocc)
self.ooov[p0:p1] = ov.reshape(p1 - p0, nocc, nocc, nvir)
oovv[p0:p1] = lib.unpack_tril(vv, out=buf).reshape(
p1 - p0, nocc, nvir, nvir)
def save_vir_frac(p0, p1, eri):
oo, ov, vv = sort_inplace(p0, p1, eri)
self.vooo[p0:p1] = lib.unpack_tril(oo, out=buf).reshape(
p1 - p0, nocc, nocc, nocc)
self.voov[p0:p1] = ov.reshape(p1 - p0, nocc, nocc, nvir)
self.vovv[p0:p1] = vv.reshape(p1 - p0, nocc, -1)
if not myci.direct:
max_memory = max(2000,
myci.max_memory - lib.current_memory()[0])
self.feri2 = lib.H5TmpFile()
ao2mo.full(myci.mol,
orbv,
self.feri2,
max_memory=max_memory,
verbose=log)
self.vvvv = self.feri2['eri_mo']
cput1 = log.timer_debug1('transforming vvvv', *cput1)
tmpfile3 = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
with h5py.File(tmpfile3.name, 'w') as feri:
max_memory = max(2000,
myci.max_memory - lib.current_memory()[0])
mo = numpy.hstack((orbv, orbo))
ao2mo.general(myci.mol, (mo, orbo, mo, mo),
feri,
max_memory=max_memory,
verbose=log)
cput1 = log.timer_debug1('transforming oppp', *cput1)
blksize = max(
1, int(min(8e9, max_memory * .5e6) / 8 / nmo**2 / nocc))
handler = None
for p0, p1 in lib.prange(0, nvir, blksize):
eri = _cp(feri['eri_mo'][p0 * nocc:p1 * nocc])
handler = async_do(handler, save_vir_frac, p0, p1, eri)
for p0, p1 in lib.prange(0, nocc, blksize):
eri = _cp(feri['eri_mo'][(p0 + nvir) * nocc:(p1 + nvir) *
nocc])
handler = async_do(handler, save_occ_frac, p0, p1, eri)
if handler is not None:
handler.join()
self.vvoo[:] = lib.transpose(oovv.reshape(nocc**2, -1)).reshape(
nvir, nvir, nocc, nocc)
log.timer('CISD integral transformation', *cput0)
def __init__(self, myci, mo_coeff=None, method='incore'):
cput0 = (time.clock(), time.time())
moidx = numpy.ones(myci.mo_occ.size, dtype=numpy.bool)
if isinstance(myci.frozen, (int, numpy.integer)):
moidx[:myci.frozen] = False
elif len(myci.frozen) > 0:
moidx[numpy.asarray(myci.frozen)] = False
if mo_coeff is None:
self.mo_coeff = mo_coeff = myci.mo_coeff[:,moidx]
else:
self.mo_coeff = mo_coeff = mo_coeff[:,moidx]
dm = myci._scf.make_rdm1(myci.mo_coeff, myci.mo_occ)
fockao = myci._scf.get_hcore() + myci._scf.get_veff(myci.mol, dm)
self.fock = reduce(numpy.dot, (mo_coeff.T, fockao, mo_coeff))
nocc = myci.nocc
nmo = myci.nmo
nvir = nmo - nocc
mem_incore, mem_outcore, mem_basic = ccsd._mem_usage(nocc, nvir)
mem_now = lib.current_memory()[0]
log = logger.Logger(myci.stdout, myci.verbose)
if (method == 'incore' and myci._scf._eri is not None and
(mem_incore+mem_now < myci.max_memory) or myci.mol.incore_anyway):
eri1 = ao2mo.incore.full(myci._scf._eri, mo_coeff)
#:eri1 = ao2mo.restore(1, eri1, nmo)
#:self.oooo = eri1[:nocc,:nocc,:nocc,:nocc].copy()
#:self.ooov = eri1[:nocc,:nocc,:nocc,nocc:].copy()
#:self.vooo = eri1[nocc:,:nocc,:nocc,:nocc].copy()
#:self.voov = eri1[nocc:,:nocc,:nocc,nocc:].copy()
#:self.vvoo = eri1[nocc:,nocc:,:nocc,:nocc].copy()
#:vovv = eri1[nocc:,:nocc,nocc:,nocc:].copy()
#:self.vovv = lib.pack_tril(vovv.reshape(-1,nvir,nvir))
#:self.vvvv = ao2mo.restore(4, eri1[nocc:,nocc:,nocc:,nocc:], nvir)
nvir_pair = nvir * (nvir+1) // 2
self.oooo = numpy.empty((nocc,nocc,nocc,nocc))
self.ooov = numpy.empty((nocc,nocc,nocc,nvir))
self.vooo = numpy.empty((nvir,nocc,nocc,nocc))
self.voov = numpy.empty((nvir,nocc,nocc,nvir))
self.vovv = numpy.empty((nvir,nocc,nvir_pair))
self.vvvv = numpy.empty((nvir_pair,nvir_pair))
ij = 0
outbuf = numpy.empty((nmo,nmo,nmo))
oovv = numpy.empty((nocc,nocc,nvir,nvir))
for i in range(nocc):
buf = lib.unpack_tril(eri1[ij:ij+i+1], out=outbuf[:i+1])
for j in range(i+1):
self.oooo[i,j] = self.oooo[j,i] = buf[j,:nocc,:nocc]
self.ooov[i,j] = self.ooov[j,i] = buf[j,:nocc,nocc:]
oovv[i,j] = oovv[j,i] = buf[j,nocc:,nocc:]
ij += i + 1
self.vvoo = lib.transpose(oovv.reshape(nocc**2,-1)).reshape(nvir,nvir,nocc,nocc)
oovv = None
ij1 = 0
for i in range(nocc,nmo):
buf = lib.unpack_tril(eri1[ij:ij+i+1], out=outbuf[:i+1])
self.vooo[i-nocc] = buf[:nocc,:nocc,:nocc]
self.voov[i-nocc] = buf[:nocc,:nocc,nocc:]
lib.pack_tril(_cp(buf[:nocc,nocc:,nocc:]), out=self.vovv[i-nocc])
dij = i - nocc + 1
lib.pack_tril(_cp(buf[nocc:i+1,nocc:,nocc:]),
out=self.vvvv[ij1:ij1+dij])
ij += i + 1
ij1 += dij
else:
cput1 = time.clock(), time.time()
_tmpfile1 = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
_tmpfile2 = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
self.feri1 = feri1 = h5py.File(_tmpfile1.name)
def __del__feri1(self):
feri1.close()
self.feri1.__del__ = __del__feri1
orbo = mo_coeff[:,:nocc]
orbv = mo_coeff[:,nocc:]
nvpair = nvir * (nvir+1) // 2
self.oooo = self.feri1.create_dataset('oooo', (nocc,nocc,nocc,nocc), 'f8')
self.ooov = self.feri1.create_dataset('ooov', (nocc,nocc,nocc,nvir), 'f8')
self.vvoo = self.feri1.create_dataset('vvoo', (nvir,nvir,nocc,nocc), 'f8')
self.vooo = self.feri1.create_dataset('vooo', (nvir,nocc,nocc,nocc), 'f8')
self.voov = self.feri1.create_dataset('voov', (nvir,nocc,nocc,nvir), 'f8')
self.vovv = self.feri1.create_dataset('vovv', (nvir,nocc,nvpair), 'f8')
fsort = _ccsd.libcc.CCsd_sort_inplace
nocc_pair = nocc*(nocc+1)//2
nvir_pair = nvir*(nvir+1)//2
def sort_inplace(p0, p1, eri):
fsort(eri.ctypes.data_as(ctypes.c_void_p),
ctypes.c_int(nocc), ctypes.c_int(nvir),
ctypes.c_int((p1-p0)*nocc))
vv = eri[:,:nvir_pair]
oo = eri[:,nvir_pair:nvir_pair+nocc_pair]
ov = eri[:,nvir_pair+nocc_pair:].reshape(-1,nocc,nvir)
return oo, ov, vv
buf = numpy.empty((nmo,nmo,nmo))
oovv = numpy.empty((nocc,nocc,nvir,nvir))
def save_occ_frac(p0, p1, eri):
oo, ov, vv = sort_inplace(p0, p1, eri)
self.oooo[p0:p1] = lib.unpack_tril(oo, out=buf).reshape(p1-p0,nocc,nocc,nocc)
self.ooov[p0:p1] = ov.reshape(p1-p0,nocc,nocc,nvir)
oovv[p0:p1] = lib.unpack_tril(vv, out=buf).reshape(p1-p0,nocc,nvir,nvir)
def save_vir_frac(p0, p1, eri):
oo, ov, vv = sort_inplace(p0, p1, eri)
self.vooo[p0:p1] = lib.unpack_tril(oo, out=buf).reshape(p1-p0,nocc,nocc,nocc)
self.voov[p0:p1] = ov.reshape(p1-p0,nocc,nocc,nvir)
self.vovv[p0:p1] = vv.reshape(p1-p0,nocc,-1)
if not myci.direct:
max_memory = max(2000,myci.max_memory-lib.current_memory()[0])
self.feri2 = feri2 = h5py.File(_tmpfile2.name)
def __del__feri2(self):
feri2.close()
self.feri2.__del__ = __del__feri2
ao2mo.full(myci.mol, orbv, self.feri2, max_memory=max_memory, verbose=log)
self.vvvv = self.feri2['eri_mo']
cput1 = log.timer_debug1('transforming vvvv', *cput1)
tmpfile3 = tempfile.NamedTemporaryFile(dir=lib.param.TMPDIR)
with h5py.File(tmpfile3.name, 'w') as feri:
max_memory = max(2000, myci.max_memory-lib.current_memory()[0])
mo = numpy.hstack((orbv, orbo))
ao2mo.general(myci.mol, (mo,orbo,mo,mo),
feri, max_memory=max_memory, verbose=log)
cput1 = log.timer_debug1('transforming oppp', *cput1)
blksize = max(1, int(min(8e9,max_memory*.5e6)/8/nmo**2/nocc))
handler = None
for p0, p1 in lib.prange(0, nvir, blksize):
eri = _cp(feri['eri_mo'][p0*nocc:p1*nocc])
handler = async_do(handler, save_vir_frac, p0, p1, eri)
for p0, p1 in lib.prange(0, nocc, blksize):
eri = _cp(feri['eri_mo'][(p0+nvir)*nocc:(p1+nvir)*nocc])
handler = async_do(handler, save_occ_frac, p0, p1, eri)
if handler is not None:
handler.join()
self.vvoo[:] = lib.transpose(oovv.reshape(nocc**2,-1)).reshape(nvir,nvir,nocc,nocc)
log.timer('CISD integral transformation', *cput0)