def _make_eris_outcore(mycc, mo_coeff=None):
cput0 = (logger.process_clock(), logger.perf_counter())
log = logger.Logger(mycc.stdout, mycc.verbose)
eris = _ChemistsERIs()
eris._common_init_(mycc, mo_coeff)
mol = mycc.mol
mo_coeff = eris.mo_coeff
nocc = eris.nocc
nao, nmo = mo_coeff.shape
nvir = nmo - nocc
eris.feri1 = lib.H5TmpFile()
eris.oooo = eris.feri1.create_dataset('oooo', (nocc, nocc, nocc, nocc),
'f8')
eris.ovoo = eris.feri1.create_dataset('ovoo', (nocc, nvir, nocc, nocc),
'f8',
chunks=(nocc, 1, nocc, nocc))
eris.ovov = eris.feri1.create_dataset('ovov', (nocc, nvir, nocc, nvir),
'f8',
chunks=(nocc, 1, nocc, nvir))
eris.ovvo = eris.feri1.create_dataset('ovvo', (nocc, nvir, nvir, nocc),
'f8',
chunks=(nocc, 1, nvir, nocc))
eris.ovvv = eris.feri1.create_dataset('ovvv', (nocc, nvir, nvir, nvir),
'f8')
eris.oovv = eris.feri1.create_dataset('oovv', (nocc, nocc, nvir, nvir),
'f8',
chunks=(nocc, nocc, 1, nvir))
max_memory = max(MEMORYMIN, mycc.max_memory - lib.current_memory()[0])
ftmp = lib.H5TmpFile()
ao2mo.full(mol, mo_coeff, ftmp, max_memory=max_memory, verbose=log)
eri = ftmp['eri_mo']
nocc_pair = nocc * (nocc + 1) // 2
tril2sq = lib.square_mat_in_trilu_indices(nmo)
oo = eri[:nocc_pair]
eris.oooo[:] = ao2mo.restore(1, oo[:, :nocc_pair], nocc)
oovv = lib.take_2d(oo, tril2sq[:nocc, :nocc].ravel(),
tril2sq[nocc:, nocc:].ravel())
eris.oovv[:] = oovv.reshape(nocc, nocc, nvir, nvir)
oo = oovv = None
tril2sq = lib.square_mat_in_trilu_indices(nmo)
blksize = min(nvir, max(BLKMIN, int(max_memory * 1e6 / 8 / nmo**3 / 2)))
for p0, p1 in lib.prange(0, nvir, blksize):
q0, q1 = p0 + nocc, p1 + nocc
off0 = q0 * (q0 + 1) // 2
off1 = q1 * (q1 + 1) // 2
buf = lib.unpack_tril(eri[off0:off1])
tmp = buf[tril2sq[q0:q1, :nocc] - off0]
eris.ovoo[:, p0:p1] = tmp[:, :, :nocc, :nocc].transpose(1, 0, 2, 3)
eris.ovvo[:, p0:p1] = tmp[:, :, nocc:, :nocc].transpose(1, 0, 2, 3)
eris.ovov[:, p0:p1] = tmp[:, :, :nocc, nocc:].transpose(1, 0, 2, 3)
eris.ovvv[:, p0:p1] = tmp[:, :, nocc:, nocc:].transpose(1, 0, 2, 3)
buf = tmp = None
log.timer('GW integral transformation', *cput0)
return eris
def create_t3_eris(mycc, kconserv, eris, tmpfile='tmp_t3_eris.h5'):
'''Create/transpose necessary eri integrals needed for fast read-in by CCSD(T).'''
eris_vovv, eris_oovv, eris_ooov, t2 = eris
nkpts = mycc.nkpts
nocc = mycc.nocc
nmo = mycc.nmo
nvir = nmo - nocc
nmo = nocc + nvir
feri_tmp = None
h5py_kwargs = {}
feri_tmp_filename = tmpfile
dtype = np.result_type(eris_vovv, eris_oovv, eris_ooov, t2)
if not check_read_success(feri_tmp_filename):
feri_tmp = lib.H5TmpFile(feri_tmp_filename, 'w', **h5py_kwargs)
t2T_out = feri_tmp.create_dataset(
't2T', (nkpts, nkpts, nkpts, nvir, nvir, nocc, nocc),
dtype=dtype) # noqa: E501
eris_vvop_out = feri_tmp.create_dataset(
'vvop', (nkpts, nkpts, nkpts, nvir, nvir, nocc, nmo),
dtype=dtype) # noqa: E501
eris_vooo_C_out = feri_tmp.create_dataset(
'vooo_C', (nkpts, nkpts, nkpts, nvir, nocc, nocc, nocc),
dtype=dtype) # noqa: E501
transpose_t2(t2, nkpts, nocc, nvir, kconserv, out=t2T_out)
create_eris_vvop(eris_vovv,
eris_oovv,
nkpts,
nocc,
nvir,
kconserv,
out=eris_vvop_out)
create_eris_vooo(eris_ooov,
nkpts,
nocc,
nvir,
kconserv,
out=eris_vooo_C_out)
feri_tmp.attrs['completed'] = True
feri_tmp.close()
feri_tmp = lib.H5TmpFile(feri_tmp_filename, 'r', **h5py_kwargs)
t2T = feri_tmp['t2T']
eris_vvop = feri_tmp['vvop']
eris_vooo_C = feri_tmp['vooo_C']
mem_now = lib.current_memory()[0]
max_memory = max(0, mycc.max_memory - mem_now)
unit = nkpts**3 * (nvir**2 * nocc**2 + nvir**2 * nmo * nocc +
nvir * nocc**3)
if (unit * 16 < max_memory): # Store all in memory
t2T = t2T[:]
eris_vvop = eris_vvop[:]
eris_vooo_C = eris_vooo_C[:]
return feri_tmp, t2T, eris_vvop, eris_vooo_C
def _store(self, key, value):
if self._diisfile is None:
if isinstance(self.filename, str):
filename = self.filename + '__rank' + str(mpi.rank)
self._diisfile = lib.H5TmpFile(filename, 'w')
elif not (self.incore or value.size < lib.diis.INCORE_SIZE):
self._diisfile = lib.H5TmpFile(self.filename, 'w')
return lib.diis.DIIS._store(self, key, value)
def test_r_outcore_eri(self):
n2c = mol.nao_2c()
numpy.random.seed(1)
mo = numpy.random.random((n2c,n2c)) + numpy.random.random((n2c,n2c))*1j
eriref = trans(eri0, [mo]*4)
ftmp = tempfile.NamedTemporaryFile()
ao2mo.kernel(mol, mo, erifile=ftmp.name, intor='int2e_spinor', max_memory=10, ioblk_size=5)
with ao2mo.load(ftmp) as eri1:
self.assertAlmostEqual(lib.finger(eri1), -550.72966498073129-1149.3561026721848j, 8)
self.assertAlmostEqual(abs(eri1-eriref.reshape(n2c**2,n2c**2)).max(), 0, 9)
eri1 = ao2mo.kernel(mol, (mo[:,:2], mo[:,:4], mo[:,:2], mo[:,:4]),
erifile=ftmp.name, intor='int2e_spinor')
with ao2mo.load(ftmp) as eri1:
self.assertAlmostEqual(abs(eri1-eriref[:2,:4,:2,:4].reshape(8,8)).max(), 0, 9)
ftmp = lib.H5TmpFile()
ao2mo.kernel(mol, (mo[:,:2], mo[:,:4], mo[:,:2], mo[:,:4]),
erifile=ftmp, intor='int2e_spinor', aosym='s1')
with ao2mo.load(ftmp) as eri1:
self.assertAlmostEqual(abs(eri1-eriref[:2,:4,:2,:4].reshape(8,8)).max(), 0, 9)
eri1 = ao2mo.kernel(mol, (mo[:,:2], mo[:,:4], mo[:,:4], mo[:,:2]),
intor='int2e_spinor', aosym='s2ij')
self.assertAlmostEqual(abs(eri1-eriref[:2,:4,:4,:2].reshape(8,8)).max(), 0, 9)
eri1 = ao2mo.kernel(mol, (mo[:,:2], mo[:,:4], mo[:,:2], mo[:,:4]),
intor='int2e_spinor', aosym='s2kl')
self.assertAlmostEqual(abs(eri1-eriref[:2,:4,:2,:4].reshape(8,8)).max(), 0, 9)
eri1 = ao2mo.kernel(mol, mo[:,:0], intor='int2e_spinor')
self.assertTrue(eri1.size == 0)
def _gamma2_intermediates(mycc, t1, t2, l1, l2, compress_vvvv=False):
f = lib.H5TmpFile()
_gamma2_outcore(mycc, t1, t2, l1, l2, f, compress_vvvv)
d2 = (f['dovov'].value, f['dvvvv'].value, f['doooo'].value,
f['doovv'].value, f['dovvo'].value, None, f['dovvv'].value,
f['dooov'].value)
return d2
def grad_elec(cc_grad,
t1=None,
t2=None,
l1=None,
l2=None,
eris=None,
atmlst=None,
verbose=lib.logger.INFO):
mycc = cc_grad.base
if t1 is None: t1 = mycc.t1
if t2 is None: t2 = mycc.t2
if l1 is None: l1 = mycc.l1
if l2 is None: l2 = mycc.l2
if eris is None: eris = mycc.ao2mo()
d1 = uccsd_t_rdm._gamma1_intermediates(mycc,
t1,
t2,
l1,
l2,
eris,
for_grad=True)
fd2intermediate = lib.H5TmpFile()
d2 = uccsd_t_rdm._gamma2_outcore(mycc, t1, t2, l1, l2, eris,
fd2intermediate, True)
cc_grad = uccsd_grad.Gradients(mycc)
de = uccsd_grad.grad_elec(cc_grad, t1, t2, l1, l2, eris, atmlst, d1, d2,
verbose)
return de
def _make_mo_eris_outcore(agf2, mo_coeff=None):
''' Returns _ChemistsERIs
'''
cput0 = (logger.process_clock(), logger.perf_counter())
log = logger.Logger(agf2.stdout, agf2.verbose)
eris = _ChemistsERIs()
eris._common_init_(agf2, mo_coeff)
mol = agf2.mol
mo_coeff = np.asarray(eris.mo_coeff, order='F')
eris.feri = lib.H5TmpFile()
ao2mo.outcore.full(mol,
mo_coeff,
eris.feri,
dataname='mo',
max_memory=agf2.max_memory,
verbose=log)
eris.eri = eris.feri['mo']
log.timer('MO integral transformation', *cput0)
return eris
def setweights(self):
logger.info(self,
'Getting atomic data and weigths from tabulated densities')
npoints = len(self.grids.weights)
output = numpy.zeros(npoints)
promol = numpy.zeros(npoints)
ftmp = lib.H5TmpFile()
rhoat = 0.0
for i in range(self.natm):
libaim.eval_atomic(ctypes.c_int(npoints),
ctypes.c_int(self.charges[i]),
self.coords[i].ctypes.data_as(ctypes.c_void_p),
self.grids.coords.ctypes.data_as(ctypes.c_void_p),
output.ctypes.data_as(ctypes.c_void_p))
h5dat = ftmp.create_dataset('atom' + str(i), (npoints, ), 'f8')
h5dat[:] = output[:]
rhoa = numpy.einsum('i,i->', output, self.grids.weights)
rhoat += rhoa
promol += output
logger.info(self, 'Integral of rho for atom %d %f' % (i, rhoa))
logger.info(self, 'Integral of rho promolecular %f' % rhoat)
for i in range(self.natm):
h5dat = ftmp.create_dataset('weight' + str(i), (npoints, ), 'f8')
h5dat[:] = ftmp['atom' + str(i)][:] / (promol + HMINIMAL)
return ftmp
def _make_mo_eris_outcore(agf2, mo_coeff=None):
''' Returns _ChemistsERIs
'''
cput0 = (time.clock(), time.time())
log = logger.Logger(agf2.stdout, agf2.verbose)
eris = _ChemistsERIs()
eris._common_init_(agf2, mo_coeff)
mol = agf2.mol
moa = np.asarray(eris.mo_coeff[0], order='F')
mob = np.asarray(eris.mo_coeff[1], order='F')
naoa, naob = moa.shape[0], mob.shape[0]
nmoa, nmob = eris.nmo
eris.feri = lib.H5TmpFile()
ao2mo.outcore.full(mol, moa, eris.feri, dataname='mo/aa')
ao2mo.outcore.full(mol, mob, eris.feri, dataname='mo/bb')
ao2mo.outcore.general(mol, (moa,moa,mob,mob), eris.feri, dataname='mo/ab', verbose=log)
ao2mo.outcore.general(mol, (mob,mob,moa,moa), eris.feri, dataname='mo/ba', verbose=log)
eris.eri_aa = eris.feri['mo/aa']
eris.eri_ab = eris.feri['mo/ab']
eris.eri_ba = eris.feri['mo/ba']
eris.eri_bb = eris.feri['mo/bb']
eris.eri = ((eris.eri_aa, eris.eri_ab), (eris.eri_ba, eris.eri_bb))
return eris
def _make_eris_outcore(mp, mo_coeff=None, verbose=None):
cput0 = (time.clock(), time.time())
log = logger.Logger(mp.stdout, mp.verbose)
eris = _PhysicistsERIs(mp, mo_coeff)
nocc = mp.nocc
nao, nmo = eris.mo_coeff.shape
nvir = nmo - nocc
orbo = eris.mo_coeff[:, :nocc]
orbv = eris.mo_coeff[:, nocc:]
fswap = eris.feri = lib.H5TmpFile()
eris.oovv = fswap.create_dataset('oovv', (nocc, nocc, nvir, nvir), 'c8')
max_memory = mp.max_memory - lib.current_memory()[0]
blksize = min(nocc, max(2,
int(max_memory * 1e6 / 8 / (nocc * nvir**2 * 2))))
max_memory = max(2000, max_memory)
ao2mo.kernel(mp.mol, (orbo, orbv, orbo, orbv),
fswap,
max_memory=max_memory,
verbose=log,
intor='int2e_spinor')
for p0, p1 in lib.prange(0, nocc, blksize):
tmp = numpy.asarray(fswap['eri_mo'][p0 * nvir:p1 * nvir])
tmp = tmp.reshape(p1 - p0, nvir, nocc, nvir)
eris.oovv[p0:p1] = tmp.transpose(0, 2, 1, 3) - tmp.transpose(
0, 2, 3, 1)
tmp = None
cput0 = log.timer_debug1('transforming oovv', *cput0)
return eris
def __init__(self, casscf, mo, method='incore', level=1):
mol = casscf.mol
nao, nmo = mo.shape
ncore = casscf.ncore
ncas = casscf.ncas
dm_core = numpy.dot(mo[:,:ncore], mo[:,:ncore].T)
vj, vk = casscf._scf.get_jk(mol, dm_core)
self.vhf_c = reduce(numpy.dot, (mo.T, vj*2-vk, mo))
mem_incore, mem_outcore, mem_basic = _mem_usage(ncore, ncas, nmo)
mem_now = lib.current_memory()[0]
eri = casscf._scf._eri
if (method == 'incore' and eri is not None and
(mem_incore+mem_now < casscf.max_memory*.9) or
mol.incore_anyway):
if eri is None:
eri = mol.intor('int2e', aosym='s8')
self.j_pc, self.k_pc, self.ppaa, self.papa = \
trans_e1_incore(eri, mo, ncore, ncas)
else:
import gc
gc.collect()
log = logger.Logger(casscf.stdout, casscf.verbose)
self.feri = lib.H5TmpFile()
max_memory = max(3000, casscf.max_memory*.9-mem_now)
if max_memory < mem_basic:
log.warn('Calculation needs %d MB memory, over CASSCF.max_memory (%d MB) limit',
(mem_basic+mem_now)/.9, casscf.max_memory)
self.j_pc, self.k_pc = \
trans_e1_outcore(mol, mo, ncore, ncas, self.feri,
max_memory=max_memory,
level=level, verbose=log)
self.ppaa = self.feri['ppaa']
self.papa = self.feri['papa']
def kernel(mycc,
t1=None,
t2=None,
l1=None,
l2=None,
eris=None,
atmlst=None,
mf_grad=None,
verbose=lib.logger.INFO):
if t1 is None: t1 = mycc.t1
if t2 is None: t2 = mycc.t2
if l1 is None: l1 = mycc.l1
if l2 is None: l2 = mycc.l2
d1 = uccsd_t_rdm._gamma1_intermediates(mycc,
t1,
t2,
l1,
l2,
eris,
for_grad=True)
fd2intermediate = lib.H5TmpFile()
d2 = uccsd_t_rdm._gamma2_outcore(mycc, t1, t2, l1, l2, eris,
fd2intermediate, True)
return uccsd_grad.kernel(mycc, t1, t2, l1, l2, eris, atmlst, mf_grad, d1,
d2, verbose)
def _gamma2_intermediates(myci, civec, nmo, nocc, compress_vvvv=False):
f = lib.H5TmpFile()
_gamma2_outcore(myci, civec, nmo, nocc, f, compress_vvvv)
d2 = (f['dovov'].value, f['dvvvv'].value, f['doooo'].value,
f['doovv'].value, f['dovvo'].value, None, f['dovvv'].value,
f['dooov'].value)
return d2
def test_mp2_ao2mo_ovov(self):
pt = mp.mp2.MP2(mf)
orbo = mf.mo_coeff[:, :8]
orbv = mf.mo_coeff[:, 8:]
ftmp = lib.H5TmpFile()
h5dat = mp.mp2._ao2mo_ovov(pt, orbo, orbv, ftmp, 1)
ovov = numpy.asarray(h5dat)
ovov_ref = ao2mo.general(mf._eri, (orbo, orbv, orbo, orbv))
self.assertAlmostEqual(numpy.linalg.norm(ovov_ref - ovov), 0, 9)
def start(self, interval=0.02):
mycc = self._cc
log = logger.new_logger(mycc)
cpu1 = (logger.process_clock(), logger.perf_counter())
eris = mycc._eris
t2T = mycc.t2.transpose(2, 3, 0, 1)
nocc, nvir = mycc.t1.shape
nmo = nocc + nvir
vloc0, vloc1 = self.vranges[rank]
nvir_seg = vloc1 - vloc0
max_memory = min(24000, mycc.max_memory - lib.current_memory()[0])
blksize = min(
nvir_seg // 4 + 1,
max(16, int(max_memory * .3e6 / 8 / (nvir * nocc * nmo))))
self.eri_tmp = lib.H5TmpFile()
vvop = self.eri_tmp.create_dataset('vvop', (nvir_seg, nvir, nocc, nmo),
'f8')
def save_vvop(j0, j1, vvvo):
buf = numpy.empty((j1 - j0, nvir, nocc, nmo), dtype=t2T.dtype)
buf[:, :, :, :nocc] = eris.ovov[:, j0:j1].conj().transpose(
1, 3, 0, 2)
for k, (q0, q1) in enumerate(self.vranges):
blk = vvvo[k].reshape(q1 - q0, nvir, j1 - j0, nocc)
buf[:, q0:q1, :, nocc:] = blk.transpose(2, 0, 3, 1)
vvop[j0:j1] = buf
with lib.call_in_background(save_vvop) as save_vvop:
for p0, p1 in mpi.prange(vloc0, vloc1, blksize):
j0, j1 = p0 - vloc0, p1 - vloc0
sub_locs = comm.allgather((p0, p1))
vvvo = mpi.alltoall_new(
[eris.vvvo[:, :, q0:q1] for q0, q1 in sub_locs],
split_recvbuf=True)
save_vvop(j0, j1, vvvo)
cpu1 = log.timer_debug1('transpose %d:%d' % (p0, p1), *cpu1)
def send_data():
while True:
while comm.Iprobe(source=MPI.ANY_SOURCE, tag=INQUIRY):
tensors, dest = comm.recv(source=MPI.ANY_SOURCE,
tag=INQUIRY)
for task, slices in tensors:
if task == 'Done':
return
else:
mpi.send(self._get_tensor(task, slices),
dest,
tag=TRANSFER_DATA)
time.sleep(interval)
daemon = threading.Thread(target=send_data)
daemon.start()
return daemon
def _make_eris(mp, mo_coeff=None, ao2mofn=None, verbose=None):
log = logger.new_logger(mp, verbose)
time0 = (time.clock(), time.time())
eris = _ChemistsERIs()
eris._common_init_(mp, mo_coeff)
nocca, noccb = mp.get_nocc()
nmoa, nmob = mp.get_nmo()
nvira, nvirb = nmoa-nocca, nmob-noccb
nao = eris.mo_coeff[0].shape[0]
nmo_pair = nmoa * (nmoa+1) // 2
nao_pair = nao * (nao+1) // 2
mem_incore = (nao_pair**2 + nmo_pair**2) * 8/1e6
mem_now = lib.current_memory()[0]
max_memory = max(0, mp.max_memory-mem_now)
moa = eris.mo_coeff[0]
mob = eris.mo_coeff[1]
orboa = moa[:,:nocca]
orbob = mob[:,:noccb]
orbva = moa[:,nocca:]
orbvb = mob[:,noccb:]
if (mp.mol.incore_anyway or
(mp._scf._eri is not None and mem_incore+mem_now < mp.max_memory)):
log.debug('transform (ia|jb) incore')
if callable(ao2mofn):
eris.ovov = ao2mofn((orboa,orbva,orboa,orbva)).reshape(nocca*nvira,nocca*nvira)
eris.ovOV = ao2mofn((orboa,orbva,orbob,orbvb)).reshape(nocca*nvira,noccb*nvirb)
eris.OVOV = ao2mofn((orbob,orbvb,orbob,orbvb)).reshape(noccb*nvirb,noccb*nvirb)
else:
eris.ovov = ao2mo.general(mp._scf._eri, (orboa,orbva,orboa,orbva))
eris.ovOV = ao2mo.general(mp._scf._eri, (orboa,orbva,orbob,orbvb))
eris.OVOV = ao2mo.general(mp._scf._eri, (orbob,orbvb,orbob,orbvb))
elif getattr(mp._scf, 'with_df', None):
logger.warn(mp, 'UMP2 detected DF being used in the HF object. '
'MO integrals are computed based on the DF 3-index tensors.\n'
'It\'s recommended to use DF-UMP2 module.')
log.debug('transform (ia|jb) with_df')
eris.ovov = mp._scf.with_df.ao2mo((orboa,orbva,orboa,orbva))
eris.ovOV = mp._scf.with_df.ao2mo((orboa,orbva,orbob,orbvb))
eris.OVOV = mp._scf.with_df.ao2mo((orbob,orbvb,orbob,orbvb))
else:
log.debug('transform (ia|jb) outcore')
eris.feri = lib.H5TmpFile()
_ao2mo_ovov(mp, (orboa,orbva,orbob,orbvb), eris.feri,
max(2000, max_memory), log)
eris.ovov = eris.feri['ovov']
eris.ovOV = eris.feri['ovOV']
eris.OVOV = eris.feri['OVOV']
time1 = log.timer('Integral transformation', *time0)
return eris
def _make_qmo_eris_outcore(agf2, eri, coeffs):
''' Returns H5 dataset
'''
cput0 = (logger.process_clock(), logger.perf_counter())
log = logger.Logger(agf2.stdout, agf2.verbose)
nmo = eri.nmo
ci, cj, ca = coeffs
ni = ci.shape[1]
nj = cj.shape[1]
na = ca.shape[1]
npair = nmo * (nmo + 1) // 2
mask = get_frozen_mask(agf2)
frozen = np.sum(~mask)
# possible to have incore MO, outcore QMO
if getattr(eri, 'feri', None) is None:
eri.feri = lib.H5TmpFile()
elif 'qmo' in eri.feri:
del eri.feri['qmo']
eri.feri.create_dataset('qmo', (nmo - frozen, ni, nj, na), 'f8')
blksize = _agf2.get_blksize(agf2.max_memory, (nmo * npair, nj * na, npair),
(nmo * ni, nj * na))
blksize = min(nmo, max(BLKMIN, blksize))
log.debug1('blksize (ragf2._make_qmo_eris_outcore) = %d', blksize)
tril2sq = lib.square_mat_in_trilu_indices(nmo)
q1 = 0
for p0, p1 in lib.prange(0, nmo, blksize):
if not np.any(mask[p0:p1]):
# block is fully frozen
continue
inds = np.arange(p0, p1)[mask[p0:p1]]
q0, q1 = q1, q1 + len(inds)
idx = list(np.concatenate(tril2sq[inds]))
buf = eri.eri[idx] # (blk, nmo, npair)
buf = buf.reshape((q1 - q0) * nmo, -1) # (blk*nmo, npair)
jasym, nja, cja, sja = ao2mo.incore._conc_mos(cj, ca, compact=True)
buf = ao2mo._ao2mo.nr_e2(buf, cja, sja, 's2kl', 's1')
buf = buf.reshape(q1 - q0, nmo, nj, na)
buf = lib.einsum('xpja,pi->xija', buf, ci)
eri.feri['qmo'][q0:q1] = np.asarray(buf, order='C')
log.timer('QMO integral transformation', *cput0)
return eri.feri['qmo']
def grad_elec(cigrad, civec=None, eris=None, atmlst=None, verbose=logger.INFO):
myci = cigrad.base
if civec is None: civec = myci.ci
assert(not isinstance(civec, (list, tuple)))
nocc = myci.nocc
nmo = myci.nmo
d1 = cisd._gamma1_intermediates(myci, civec, nmo, nocc)
fd2intermediate = lib.H5TmpFile()
d2 = cisd._gamma2_outcore(myci, civec, nmo, nocc, fd2intermediate, True)
t1 = t2 = l1 = l2 = civec
return ccsd_grad.grad_elec(cigrad, t1, t2, l1, l2, eris, atmlst, d1, d2, verbose)
def make_rdm2(mycc, t1, t2, l1, l2):
r'''
Spin-traced two-particle density matrix in MO basis
dm2[p,q,r,s] = \sum_{sigma,tau} <p_sigma^\dagger r_tau^\dagger s_tau q_sigma>
Note the contraction between ERIs (in Chemist's notation) and rdm2 is
E = einsum('pqrs,pqrs', eri, rdm2)
'''
d1 = _gamma1_intermediates(mycc, t1, t2, l1, l2)
f = lib.H5TmpFile()
d2 = _gamma2_outcore(mycc, t1, t2, l1, l2, f, False)
return _make_rdm2(mycc, d1, d2, with_dm1=True, with_frozen=True)
def __init__(self, mp, mo_coeff=None, verbose=None):
cput0 = (time.clock(), time.time())
if mo_coeff is None:
self.mo_coeff = mo_coeff = _mo_without_core(mp, mp.mo_coeff)
else:
self.mo_coeff = mo_coeff = _mo_without_core(mp, mo_coeff)
nocc = mp.nocc
nmo = mp.nmo
nvir = nmo - nocc
mem_incore, mem_outcore, mem_basic = _mem_usage(nocc, nvir)
mem_now = lib.current_memory()[0]
max_memory = max(2000, mp.max_memory * .9 - mem_now)
log = logger.Logger(mp.stdout, mp.verbose)
if max_memory < mem_basic:
log.warn(
'Not enough memory for integral transformation. '
'Available mem %s MB, required mem %s MB', max_memory,
mem_basic)
time0 = (time.clock(), time.time())
co = numpy.asarray(mo_coeff[:, :nocc], order='F')
cv = numpy.asarray(mo_coeff[:, nocc:], order='F')
if hasattr(mp._scf, 'with_df') and mp._scf.with_df:
# To handle the PBC or custom 2-electron with 3-index tensor.
# Call dfmp2.MP2 for efficient DF-MP2 implementation.
log.warn(
'MP2 detected DF being bound to the HF object. '
'(ia|jb) is computed based on the DF 3-tensor integrals.\n'
'You can switch to dfmp2.MP2 for better efficiency')
log.debug('transform (ia|jb) with_df')
self.ovov = mp._scf.with_df.ao2mo((co, cv, co, cv))
elif (mp.mol.incore_anyway
or (mp._scf._eri is not None
and mem_incore + mem_now < mp.max_memory)):
log.debug('transform (ia|jb) incore')
self.ovov = ao2mo.incore.general(mp._scf._eri, (co, cv, co, cv))
else:
log.debug('transform (ia|jb) outcore')
self.feri = lib.H5TmpFile()
#ao2mo.outcore.general(mp.mol, (co,cv,co,cv), self.feri,
# max_memory=max_memory, verbose=mp.verbose)
#self.ovov = self.feri['eri_mo']
self.ovov = _ao2mo_ovov(mp, co, cv, self.feri, max_memory,
mp.verbose)
time1 = log.timer('Integral transformation', *time0)
def transform_integrals_df(myadc):
cput0 = (time.clock(), time.time())
log = logger.Logger(myadc.stdout, myadc.verbose)
mo_coeff = np.asarray(myadc.mo_coeff, order='F')
nocc = myadc._nocc
nao, nmo = mo_coeff.shape
nvir = myadc._nmo - myadc._nocc
nvir_pair = nvir*(nvir+1)//2
with_df = myadc.with_df
naux = with_df.get_naoaux()
eris = lambda:None
eris.vvvv = None
eris.ovvv = None
Loo = np.empty((naux,nocc,nocc))
Lvo = np.empty((naux,nvir,nocc))
eris.Lvv = np.empty((naux,nvir,nvir))
eris.Lov = np.empty((naux,nocc,nvir))
ijslice = (0, nmo, 0, nmo)
Lpq = None
p1 = 0
for eri1 in with_df.loop():
Lpq = ao2mo._ao2mo.nr_e2(eri1, mo_coeff, ijslice, aosym='s2', out=Lpq).reshape(-1,nmo,nmo)
p0, p1 = p1, p1 + Lpq.shape[0]
Loo[p0:p1] = Lpq[:,:nocc,:nocc]
#Lov[p0:p1] = Lpq[:,:nocc,nocc:]
eris.Lov[p0:p1] = Lpq[:,:nocc,nocc:]
Lvo[p0:p1] = Lpq[:,nocc:,:nocc]
eris.Lvv[p0:p1] = Lpq[:,nocc:,nocc:]
Loo = Loo.reshape(naux,nocc*nocc)
eris.Lov = eris.Lov.reshape(naux,nocc*nvir)
Lvo = Lvo.reshape(naux,nocc*nvir)
eris.Lvv = eris.Lvv.reshape(naux,nvir*nvir)
eris.feri1 = lib.H5TmpFile()
eris.oooo = eris.feri1.create_dataset('oooo', (nocc,nocc,nocc,nocc), 'f8')
eris.oovv = eris.feri1.create_dataset('oovv', (nocc,nocc,nvir,nvir), 'f8', chunks=(nocc,nocc,1,nvir))
eris.ovoo = eris.feri1.create_dataset('ovoo', (nocc,nvir,nocc,nocc), 'f8', chunks=(nocc,1,nocc,nocc))
eris.ovvo = eris.feri1.create_dataset('ovvo', (nocc,nvir,nvir,nocc), 'f8', chunks=(nocc,1,nvir,nocc))
eris.oooo[:] = lib.ddot(Loo.T, Loo).reshape(nocc,nocc,nocc,nocc)
eris.ovoo[:] = lib.ddot(eris.Lov.T, Loo).reshape(nocc,nvir,nocc,nocc)
eris.oovv[:] = lib.ddot(Loo.T, eris.Lvv).reshape(nocc,nocc,nvir,nvir)
eris.ovvo[:] = lib.ddot(eris.Lov.T, Lvo).reshape(nocc,nvir,nvir,nocc)
log.timer('DF-ADC integral transformation', *cput0)
return eris
def _make_eris(mp, mo_coeff=None, ao2mofn=None, verbose=None):
log = logger.new_logger(mp, verbose)
time0 = (time.clock(), time.time())
eris = _ChemistsERIs()
eris._common_init_(mp, mo_coeff)
mo_coeff = eris.mo_coeff
nocc = mp.nocc
nmo = mp.nmo
nvir = nmo - nocc
mem_incore, mem_outcore, mem_basic = _mem_usage(nocc, nvir)
mem_now = lib.current_memory()[0]
max_memory = max(0, mp.max_memory - mem_now)
if max_memory < mem_basic:
log.warn(
'Not enough memory for integral transformation. '
'Available mem %s MB, required mem %s MB', max_memory, mem_basic)
co = numpy.asarray(mo_coeff[:, :nocc], order='F')
cv = numpy.asarray(mo_coeff[:, nocc:], order='F')
if (mp.mol.incore_anyway
or (mp._scf._eri is not None and mem_incore < max_memory)):
log.debug('transform (ia|jb) incore')
if callable(ao2mofn):
eris.ovov = ao2mofn(
(co, cv, co, cv)).reshape(nocc * nvir, nocc * nvir)
else:
eris.ovov = ao2mo.general(mp._scf._eri, (co, cv, co, cv))
elif getattr(mp._scf, 'with_df', None):
# To handle the PBC or custom 2-electron with 3-index tensor.
# Call dfmp2.MP2 for efficient DF-MP2 implementation.
log.warn('DF-HF is found. (ia|jb) is computed based on the DF '
'3-tensor integrals.\n'
'You can switch to dfmp2.MP2 for better performance')
log.debug('transform (ia|jb) with_df')
eris.ovov = mp._scf.with_df.ao2mo((co, cv, co, cv))
else:
log.debug('transform (ia|jb) outcore')
eris.feri = lib.H5TmpFile()
#ao2mo.outcore.general(mp.mol, (co,cv,co,cv), eris.feri,
# max_memory=max_memory, verbose=log)
#eris.ovov = eris.feri['eri_mo']
eris.ovov = _ao2mo_ovov(mp, co, cv, eris.feri, max(2000, max_memory),
log)
time1 = log.timer('Integral transformation', *time0)
return eris
def __init__(self, cc):
self.verbose = cc.verbose
self.stdout = cc.stdout
self.t1 = cc.t1
self.t2 = cc.t2
self.eris = cc.eris
self.kconserv = cc.khelper.kconserv
self.made_ip_imds = False
self.made_ea_imds = False
self._made_shared_2e = False
# TODO: check whether to hold all stuff in memory
if getattr(self.eris, "feri1", None):
self._fimd = lib.H5TmpFile()
else:
self._fimd = None
def test_uccsd_rdm2_mo2ao(self):
mol = gto.Mole()
mol.verbose = 0
mol.atom = [[8, (0., 0., 0.)], [1, (0., -0.757, 0.587)],
[1, (0., 0.757, 0.587)]]
mol.spin = 2
mol.basis = '631g'
mol.build(0, 0)
mf = scf.UHF(mol)
mf.conv_tol_grad = 1e-8
mf.kernel()
mycc = cc.UCCSD(mf)
mycc.diis_start_cycle = 1
mycc.conv_tol = 1e-10
eris = mycc.ao2mo()
ecc, t1, t2 = mycc.kernel(eris=eris)
l1, l2 = mycc.solve_lambda(eris=eris)
fdm2 = lib.H5TmpFile()
d2 = cc.uccsd_rdm._gamma2_outcore(mycc, t1, t2, l1, l2, fdm2, True)
nao = mycc.mo_coeff[0].shape[0]
ref = cc.uccsd_rdm._make_rdm2(mycc, None, d2, with_dm1=False)
aa = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[0], mycc.mo_coeff[0],
mycc.mo_coeff[0], mycc.mo_coeff[0], mycc.mo_coeff[0])
ab = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[1], mycc.mo_coeff[0],
mycc.mo_coeff[0], mycc.mo_coeff[1], mycc.mo_coeff[1])
bb = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref[2], mycc.mo_coeff[1],
mycc.mo_coeff[1], mycc.mo_coeff[1], mycc.mo_coeff[1])
aa = aa + aa.transpose(0, 1, 3, 2)
aa = aa + aa.transpose(1, 0, 2, 3)
aa = ao2mo.restore(4, aa, nao) * .5
bb = bb + bb.transpose(0, 1, 3, 2)
bb = bb + bb.transpose(1, 0, 2, 3)
bb = ao2mo.restore(4, bb, nao) * .5
ab = ab + ab.transpose(0, 1, 3, 2)
ab = ab + ab.transpose(1, 0, 2, 3)
ab = ao2mo.restore(4, ab, nao) * .5
ref = (aa + ab, bb + ab.T)
rdm2 = uccsd_grad._rdm2_mo2ao(mycc, d2, mycc.mo_coeff)
self.assertAlmostEqual(abs(ref[0] - rdm2[0]).max(), 0, 10)
self.assertAlmostEqual(abs(ref[1] - rdm2[1]).max(), 0, 10)
uccsd_grad._rdm2_mo2ao(mycc, d2, mycc.mo_coeff, fdm2)
self.assertAlmostEqual(
abs(ref[0] - fdm2['dm2aa+ab'].value).max(), 0, 10)
self.assertAlmostEqual(
abs(ref[1] - fdm2['dm2bb+ab'].value).max(), 0, 10)
self.assertAlmostEqual(lib.finger(rdm2[0]), -1.6247203743431637, 7)
self.assertAlmostEqual(lib.finger(rdm2[1]), -0.44062825991527471, 7)
def make_rdm2(myci, civec=None, nmo=None, nocc=None):
r'''
Spin-traced two-particle density matrix in MO basis
dm2[p,q,r,s] = \sum_{sigma,tau} <p_sigma^\dagger r_tau^\dagger s_tau q_sigma>
Note the contraction between ERIs (in Chemist's notation) and rdm2 is
E = einsum('pqrs,pqrs', eri, rdm2)
'''
if civec is None: civec = myci.ci
if nmo is None: nmo = myci.nmo
if nocc is None: nocc = myci.nocc
d1 = _gamma1_intermediates(myci, civec, nmo, nocc)
f = lib.H5TmpFile()
d2 = _gamma2_outcore(myci, civec, nmo, nocc, f, False)
return ccsd_rdm._make_rdm2(myci, d1, d2, with_dm1=True, with_frozen=True)
def test_general(self):
nao = mol.nao
mo = numpy.random.random((nao, 4))
eri = mol.intor('int2e', aosym='s8')
eri = ao2mo.kernel(eri, [mo] * 4, compact=False)
self.assertEqual(eri.shape, (16, 16))
h5file = lib.H5TmpFile()
ao2mo.kernel(mol, [mo] * 4, h5file, intor='int2e', dataname='eri')
self.assertEqual(h5file['eri'].shape, (10, 10))
ftmp = tempfile.NamedTemporaryFile()
ao2mo.kernel(mol, [mo] * 4, ftmp, intor='int2e', dataname='eri')
with ao2mo.load(ftmp.name, 'eri') as eri:
self.assertEqual(eri.shape, (10, 10))
def test_ump2_ao2mo_ovov(self):
pt = mp.UMP2(mf)
nocca, noccb = mol.nelec
orboa = mf.mo_coeff[0][:, :nocca]
orbva = mf.mo_coeff[0][:, nocca:]
orbob = mf.mo_coeff[1][:, :noccb]
orbvb = mf.mo_coeff[1][:, noccb:]
orbs = (orboa, orbva, orbob, orbvb)
ftmp = lib.H5TmpFile()
mp.ump2._ao2mo_ovov(pt, orbs, ftmp, 1)
ovov = numpy.asarray(ftmp['ovov'])
ovOV = numpy.asarray(ftmp['ovOV'])
OVOV = numpy.asarray(ftmp['OVOV'])
ovov_ref = ao2mo.general(mf._eri, (orboa, orbva, orboa, orbva))
ovOV_ref = ao2mo.general(mf._eri, (orboa, orbva, orbob, orbvb))
OVOV_ref = ao2mo.general(mf._eri, (orbob, orbvb, orbob, orbvb))
self.assertAlmostEqual(numpy.linalg.norm(ovov_ref - ovov), 0, 9)
self.assertAlmostEqual(numpy.linalg.norm(ovOV_ref - ovOV), 0, 9)
self.assertAlmostEqual(numpy.linalg.norm(OVOV_ref - OVOV), 0, 9)
def save_amps(mycc, fname="fcc"):
"""
Save amplitudes to a file.
"""
_sync_(mycc)
if fname.endswith(".h5"):
fname = fname[:-3]
filename = fname + '__rank' + str(mpi.rank) + ".h5"
fcc = lib.H5TmpFile(filename, 'w')
fcc['mo_coeff'] = mycc.mo_coeff
if (getattr(mycc, "t1", None) is not None) and \
(getattr(mycc, "t2", None) is not None):
tvec = mycc.amplitudes_to_vector(mycc.t1, mycc.t2)
fcc['tvec'] = tvec
tvec = None
if (getattr(mycc, "l1", None) is not None) and \
(getattr(mycc, "l2", None) is not None):
lvec = mycc.amplitudes_to_vector(mycc.l1, mycc.l2)
fcc['lvec'] = lvec
lvec = None
def _make_shared_2e(self):
cput0 = (time.clock(), time.time())
log = logger.Logger(self.stdout, self.verbose)
t1,t2,eris = self.t1, self.t2, self.eris
kconserv = self.kconserv
# TODO: check whether to hold Wovov Wovvo in memory
if self._fimd is None:
self._fimd = lib.H5TmpFile()
nkpts, nocc, nvir = t1.shape
self._fimd.create_dataset('ovov', (nkpts,nkpts,nkpts,nocc,nvir,nocc,nvir), t1.dtype.char)
self._fimd.create_dataset('ovvo', (nkpts,nkpts,nkpts,nocc,nvir,nvir,nocc), t1.dtype.char)
# 2 virtuals
self.Wovov = imd.Wovov(t1,t2,eris,kconserv, self._fimd['ovov'])
self.Wovvo = imd.Wovvo(t1,t2,eris,kconserv, self._fimd['ovvo'])
self.Woovv = eris.oovv
log.timer('EOM-CCSD shared two-electron intermediates', *cput0)
def test_rdm2_mo2ao(self):
mycc = cc.ccsd.CCSD(mf)
mycc.conv_tol = 1e-10
mycc.diis_start_cycle = 1
eris = mycc.ao2mo()
ecc, t1, t2 = mycc.kernel(eris=eris)
l1, l2 = mycc.solve_lambda(eris=eris)
fdm2 = lib.H5TmpFile()
d2 = cc.ccsd_rdm._gamma2_outcore(mycc, t1, t2, l1, l2, fdm2, True)
nao = mycc.mo_coeff.shape[0]
ref = cc.ccsd_rdm._make_rdm2(mycc, None, d2, with_dm1=False)
ref = lib.einsum('ijkl,pi,qj,rk,sl->pqrs', ref, mycc.mo_coeff,
mycc.mo_coeff, mycc.mo_coeff, mycc.mo_coeff)
ref = ref + ref.transpose(0, 1, 3, 2)
ref = ref + ref.transpose(1, 0, 2, 3)
ref = ao2mo.restore(4, ref, nao) * .5
rdm2 = ccsd_grad._rdm2_mo2ao(mycc, d2, mycc.mo_coeff)
ccsd_grad._rdm2_mo2ao(mycc, d2, mycc.mo_coeff, fdm2)
self.assertAlmostEqual(abs(ref - rdm2).max(), 0, 10)
self.assertAlmostEqual(abs(ref - fdm2['dm2'].value).max(), 0, 10)
self.assertAlmostEqual(lib.finger(rdm2), -0.32532303057849454, 6)