def has_kpts(self, kpts):
if kpts is None:
return True
else:
kpts = numpy.asarray(kpts).reshape(-1,3)
if self.kpts_band is None:
return all((len(member(kpt, self.kpts))>0) for kpt in kpts)
else:
return all((len(member(kpt, self.kpts))>0 or
len(member(kpt, self.kpts_band))>0) for kpt in kpts)
def aoR_loop(self, gs=None, kpts=None, kpts_band=None):
cell = self.cell
if gs is None:
gs = self.gs
self.gs = gs
if kpts is None:
kpts = self.kpts
self.kpts = kpts
if kpts_band is None:
for k in range(len(kpts)):
yield k, self.atomic_orbitals[k]
else:
where = [member(k, kpts) for k in kpts_band]
where = [k_id[0] if len(k_id) > 0 else None for k_id in where]
new_kpts = [k for k, w in zip(kpts_band, where) if w is None]
coords = cell.gen_uniform_grids(gs)
if len(new_kpts) > 0:
new_ao = iter(
self._numint.eval_ao(cell,
coords,
new_kpts,
non0tab=self._numint.non0tab))
aoR = (self.atomic_orbitals[where[k]]
if not where[k] is None else next(new_ao)
for k in range(len(kpts_band)))
if kpts_band.ndim == 1:
yield 0, next(aoR)
else:
for k in range(len(kpts_band)):
yield k, next(aoR)
def __enter__(self):
self.feri = h5py.File(self.cderi, 'r')
kpti_kptj = numpy.asarray(self.kpti_kptj)
kptij_lst = self.feri['%s-kptij'%self.label].value
k_id = member(kpti_kptj, kptij_lst)
if len(k_id) > 0:
dat = self.feri['%s/%d' % (self.label,k_id[0])]
else:
# swap ki,kj due to the hermiticity
kptji = kpti_kptj[[1,0]]
k_id = member(kptji, kptij_lst)
if len(k_id) == 0:
raise RuntimeError('%s for kpts %s is not initialized.\n'
'Reset attribute .kpts then call '
'.build() to initialize %s.'
% (self.label, kpti_kptj, self.label))
dat = self.feri['%s/%d' % (self.label, k_id[0])]
dat = _load_and_unpack(dat)
return dat
def build(self, j_only=None, with_j3c=True, kpts_band=None):
if self.kpts_band is not None:
self.kpts_band = numpy.reshape(self.kpts_band, (-1, 3))
if kpts_band is not None:
kpts_band = numpy.reshape(kpts_band, (-1, 3))
if self.kpts_band is None:
self.kpts_band = kpts_band
else:
self.kpts_band = unique(
numpy.vstack((self.kpts_band, kpts_band)))[0]
self.check_sanity()
self.dump_flags()
self.auxcell = make_modrho_basis(self.cell, self.auxbasis, self.eta)
if self.kpts_band is None:
kpts = self.kpts
kband_uniq = numpy.zeros((0, 3))
else:
kpts = self.kpts
kband_uniq = [
k for k in self.kpts_band if len(member(k, kpts)) == 0
]
if j_only is None:
j_only = self._j_only
if j_only:
kall = numpy.vstack([kpts, kband_uniq])
kptij_lst = numpy.hstack((kall, kall)).reshape(-1, 2, 3)
else:
kptij_lst = [(ki, kpts[j]) for i, ki in enumerate(kpts)
for j in range(i + 1)]
kptij_lst.extend([(ki, kj) for ki in kband_uniq for kj in kpts])
kptij_lst.extend([(ki, ki) for ki in kband_uniq])
kptij_lst = numpy.asarray(kptij_lst)
if with_j3c:
if isinstance(self._cderi_to_save, str):
cderi = self._cderi_to_save
if isinstance(self._cderi, str):
logger.warn(
self, 'Value of _cderi is ignored. DF '
'integrals will be saved in file %s .', cderi)
else:
cderi = self._cderi_to_save.name
self._cderi = cderi
t1 = (time.clock(), time.time())
self._make_j3c(self.cell, self.auxcell, kptij_lst, cderi)
t1 = logger.timer_debug1(self, 'j3c', *t1)
return self
def _ewald_exxdiv_for_G0(cell, kpts, dms, vk, kpts_band=None):
s = cell.pbc_intor('int1e_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]))
def _ewald_exxdiv_for_G0(cell, kpts, dms, vk, kpts_band=None):
s = cell.pbc_intor('int1e_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)
