def nelec(self, mu):
logger.debug1(self.__log__, "| requested mu={:.3e}".format(
mu,
))
result = []
total = 0
for ind, (i, c) in enumerate(zip(self.solvers, self.factors)):
n = i.__hcore__.shape[0] // 2
i.__hcore__[:n, :n] -= numpy.eye(n) * mu
i.kernel()
i.__hcore__[:n, :n] += numpy.eye(n) * mu
dm = i.make_rdm1()
result.append(numpy.diag(dm)[:n].sum())
total += c*result[-1]
logger.debug2(self.__log__, "| solver {:d} E={:.8f}".format(
ind,
i.e_tot,
))
logger.debug1(self.__log__, "| occupations {} = {:.3e}".format(
"+".join("{:.1f}*{:.3f}".format(i, j) for i, j in zip(self.factors, result)),
total,
))
return total-self.target
def dump_flags(self, verbose=None):
logger.info(self, '******** %s ********', self.__class__)
logger.info(self, 'lebedev_order = %s (%d grids per sphere)',
self.lebedev_order, gen_grid.LEBEDEV_ORDER[self.lebedev_order])
logger.info(self, 'lmax = %s' , self.lmax)
logger.info(self, 'eta = %s' , self.eta)
logger.info(self, 'eps = %s' , self.eps)
logger.debug2(self, 'radii_table %s', self.radii_table)
if self.atom_radii:
logger.info(self, 'User specified atomic radii %s', str(self.atom_radii))
self.grids.dump_flags(verbose)
return self
def dump_flags(self, verbose=None):
logger.info(self, 'radial grids: %s', self.radi_method.__doc__)
logger.info(self, 'becke partition: %s', self.becke_scheme.__doc__)
logger.info(self, 'pruning grids: %s', self.prune)
logger.info(self, 'grids dens level: %d', self.level)
logger.info(self, 'symmetrized grids: %s', self.symmetry)
if self.radii_adjust is not None:
logger.info(self, 'atomic radii adjust function: %s',
self.radii_adjust)
logger.debug2(self, 'atomic_radii : %s', self.atomic_radii)
if self.atom_grid:
logger.info(self, 'User specified grid scheme %s', str(self.atom_grid))
return self
def sr_loop(self, kpti_kptj=numpy.zeros((2,3)), max_memory=2000,
compact=True, blksize=None):
'''Short range part'''
kpti, kptj = kpti_kptj
unpack = is_zero(kpti-kptj) and not compact
is_real = is_zero(kpti_kptj)
nao = self.cell.nao_nr()
if blksize is None:
if is_real:
if unpack:
blksize = max_memory*1e6/8/(nao*(nao+1)//2+nao**2*2)
else:
blksize = max_memory*1e6/8/(nao*(nao+1)*2)
else:
blksize = max_memory*1e6/16/(nao**2*3)
blksize = max(16, min(int(blksize), self.blockdim))
logger.debug2(self, 'max_memory %d MB, blksize %d', max_memory, blksize)
if unpack:
buf = numpy.empty((blksize,nao*(nao+1)//2))
def load(Lpq, b0, b1, bufR, bufI):
Lpq = numpy.asarray(Lpq[b0:b1])
if is_real:
if unpack:
LpqR = lib.unpack_tril(Lpq, out=bufR).reshape(-1,nao**2)
else:
LpqR = Lpq
LpqI = numpy.zeros_like(LpqR)
else:
shape = Lpq.shape
if unpack:
tmp = numpy.ndarray(shape, buffer=buf)
tmp[:] = Lpq.real
LpqR = lib.unpack_tril(tmp, out=bufR).reshape(-1,nao**2)
tmp[:] = Lpq.imag
LpqI = lib.unpack_tril(tmp, lib.ANTIHERMI, out=bufI).reshape(-1,nao**2)
else:
LpqR = numpy.ndarray(shape, buffer=bufR)
LpqR[:] = Lpq.real
LpqI = numpy.ndarray(shape, buffer=bufI)
LpqI[:] = Lpq.imag
return LpqR, LpqI
LpqR = LpqI = j3cR = j3cI = None
with self.load_Lpq(kpti_kptj) as Lpq:
naux = Lpq.shape[0]
with self.load_j3c(kpti_kptj) as j3c:
for b0, b1 in lib.prange(0, naux, blksize):
LpqR, LpqI = load(Lpq, b0, b1, LpqR, LpqI)
j3cR, j3cI = load(j3c, b0, b1, j3cR, j3cI)
yield LpqR, LpqI, j3cR, j3cI
def _ewald_exxdiv_for_G0(cell, kpts, dms, vk):
if kpts is None or numpy.shape(kpts) == (3, ):
ovlp = cell.pbc_intor('cint1e_ovlp_sph', hermi=1)
madelung = tools.pbc.madelung(cell, numpy.zeros(3))
for i, dm in enumerate(dms):
vk[i] += madelung * reduce(numpy.dot, (ovlp, dm, ovlp))
else:
ovlp = cell.pbc_intor('cint1e_ovlp_sph', hermi=1, kpts=kpts)
weight = 1. / dms.shape[1]
madelung = weight * len(kpts) * tools.pbc.madelung(cell, kpts)
for k, s in enumerate(ovlp):
for i, dm in enumerate(dms):
vk[i, k] += madelung * reduce(numpy.dot, (s, dm[k], s))
logger.debug2(
cell, 'Total energy shift = -1/2 * Nelec*madelung/cell.vol = %.12g',
madelung * cell.nelectron * -.5)
def dump_flags(self, verbose=None):
logger.info(self, '******** %s (In testing) ********', self.__class__)
logger.warn(self, 'ddPCM is an experimental feature. It is '
'still in testing.\nFeatures and APIs may be changed '
'in the future.')
logger.info(self, 'lebedev_order = %s (%d grids per sphere)',
self.lebedev_order, gen_grid.LEBEDEV_ORDER[self.lebedev_order])
logger.info(self, 'lmax = %s' , self.lmax)
logger.info(self, 'eta = %s' , self.eta)
logger.info(self, 'eps = %s' , self.eps)
logger.info(self, 'frozen = %s' , self.frozen)
logger.info(self, 'equilibrium_solvation = %s', self.equilibrium_solvation)
logger.debug2(self, 'radii_table %s', self.radii_table)
if self.atom_radii:
logger.info(self, 'User specified atomic radii %s', str(self.atom_radii))
self.grids.dump_flags(verbose)
return self
def _ewald_exxdiv_for_G0(cell, kpts, dms, vk, kpts_band=None):
s = cell.pbc_intor('cint1e_ovlp_sph', hermi=1, kpts=kpts)
madelung = tools.pbc.madelung(cell, kpts)
if kpts is None:
for i,dm in enumerate(dms):
vk[i] += madelung * reduce(numpy.dot, (s, dm, s))
elif numpy.shape(kpts) == (3,):
if kpts_band is None or is_zero(kpts_band-kpts):
for i,dm in enumerate(dms):
vk[i] += madelung * reduce(numpy.dot, (s, dm, s))
else: # kpts.shape == (*,3)
if kpts_band is None:
for k in range(len(kpts)):
for i,dm in enumerate(dms):
vk[i,k] += madelung * reduce(numpy.dot, (s[k], dm[k], s[k]))
else:
kpts_band = kpts_band.reshape(-1,3)
for k, kpt in enumerate(kpts):
for kp in member(kpt, kpts_band):
for i,dm in enumerate(dms):
vk[i,kp] += madelung * reduce(numpy.dot, (s[k], dm[k], s[k]))
logger.debug2(cell, 'Total energy shift = -1/2 * Nelec*madelung/cell.vol = %.12g',
madelung*cell.nelectron * -.5)
def kernel(self, tolerance="default", maxiter=30):
"""
Performs a self-consistent DMET calculation.
Args:
tolerance (float): convergence criterion;
maxiter (int): maximal number of iterations;
"""
if tolerance == "default":
tolerance = self.conv_tol
self.convergence_history = []
# mixers = dict((k, diis.DIIS()) for k in self.__domains__.keys())
while True:
logger.info(self.__mol__, "DMET step {:d}".format(
len(self.convergence_history),
))
mf = self.run_mf_kernel()
umat = {}
logger.debug1(self.__mol__, "Mean-field solver total energy E = {:.10f}".format(
mf.e_tot,
))
self.e_tot = 0
total_occupation = 0
domain_ids = []
embedded_solvers = []
replica_numbers = []
schmidt_bases = []
# Build embedded solvers
logger.info(self.__mol__, "Building embedded solvers ...")
for domain_id, domain_basis, schmidt_basis in self.iter_schmidt_basis():
domain_ids.append(domain_id)
if self.__style__ == "interacting-bath":
embedded_solvers.append(self.get_embedded_solver(schmidt_basis))
elif self.__style__ == "non-interacting-bath":
embedded_solvers.append(self.get_embedded_solver(schmidt_basis, kind=domain_id))
else:
raise ValueError("Internal error: unknown style '{}'".format(self.__style__))
replica_numbers.append(len(self.__domains__[domain_id]))
schmidt_bases.append(schmidt_basis[2:])
# Fit chemical potential
logger.info(self.__mol__, "Fitting chemical potential ...")
GlobalChemicalPotentialFit(
embedded_solvers,
replica_numbers,
self.__mol__.nelectron,
log=self.__mol__,
).kernel()
# Fit the u-matrix
logger.info(self.__mol__, "Fitting the u-matrix ...")
for domain_id, embedded_solver, schmidt_basis, nreplica in zip(domain_ids, embedded_solvers, schmidt_bases, replica_numbers):
logger.debug(self.__mol__, "Domain {}".format(domain_id))
logger.debug1(self.__mol__, "Primary basis: {}".format(self.__domains__[domain_id][0]))
if len(self.__domains__[domain_id]) > 1:
for i, b in enumerate(self.__domains__[domain_id][1:]):
logger.debug1(self.__mol__, "Secondary basis {:d}: {}".format(i, b))
logger.debug1(self.__mol__, "Correlated solver total energy E = {:.10f}".format(
embedded_solver.e_tot,
))
n_active_domain = schmidt_basis[0].shape[1]
# TODO: fix this; no need to recalculate hcore
partial_energy = embedded_solver.partial_etot(
slice(n_active_domain),
transform(
self.__mf_solver__.get_hcore(),
self.__orthogonal_basis_inv__.T.dot(numpy.concatenate(schmidt_basis, axis=1)),
),
)
self.e_tot += nreplica * partial_energy
logger.debug1(self.__mol__, "Correlated solver partial energy E = {:.10f}".format(
partial_energy,
))
partial_occupation = embedded_solver.partial_nelec(slice(n_active_domain))
total_occupation += nreplica * partial_occupation
logger.debug1(self.__mol__, "Correlated solver partial occupation N = {:.10f}".format(
partial_occupation,
))
logger.debug2(self.__mol__, "Correlated solver density matrix: {}".format(embedded_solver.make_rdm1()))
if tolerance is not None:
# Continue with self-consistency
nscf_mf = NonSelfConsistentMeanField(mf)
nscf_mf.kernel()
sc = self.__self_consistency__(
nscf_mf,
self.__orthogonal_basis__.dot(numpy.concatenate(schmidt_basis, axis=1)),
embedded_solver,
log=self.__mol__,
)
sc.kernel(x0=None)
local_umat = sc.parametrize_umat_full(sc.final_parameters)
umat[domain_id] = local_umat
logger.debug(self.__mol__, "Parameters: {}".format(
sc.final_parameters,
))
self.e_tot += mf.energy_nuc()
if tolerance is not None:
self.convergence_history.append(self.convergence_measure(umat))
self.umat = umat
# self.umat = dict((k, mixers[k].update(umat[k])) for k in self.__domains__.keys())
logger.info(self.__mol__, "E = {:.10f} delta = {:.3e} q = {:.3e} max(umat) = {:.3e}".format(
self.e_tot,
self.convergence_history[-1],
self.__mol__.nelectron - total_occupation,
max(v.max() for v in self.umat.values()),
))
else:
logger.info(self.__mol__, "E = {:.10f} q = {:.3e}".format(
self.e_tot,
self.__mol__.nelectron - total_occupation,
))
if tolerance is None or self.convergence_history[-1] < tolerance:
return self.e_tot
if maxiter is not None and len(self.convergence_history) >= maxiter:
raise RuntimeError("The maximal number of iterations {:d} reached. The error {:.3e} is still above the requested tolerance of {:.3e}".format(
maxiter,
self.convergence_history[-1],
tolerance,
))