def build(self,
dump_input=True,
parse_arg=True,
a=None,
gs=None,
ke_cutoff=None,
precision=None,
nimgs=None,
ew_eta=None,
ew_cut=None,
pseudo=None,
basis=None,
h=None,
dimension=None,
rcut=None,
ecp=None,
*args,
**kwargs):
'''Setup Mole molecule and Cell and initialize some control parameters.
Whenever you change the value of the attributes of :class:`Cell`,
you need call this function to refresh the internal data of Cell.
Kwargs:
a : (3,3) ndarray
The real-space unit cell lattice vectors. Each row represents
a lattice vector.
gs : (3,) ndarray of ints
The number of *positive* G-vectors along each direction.
pseudo : dict or str
To define pseudopotential. If given, overwrite :attr:`Cell.pseudo`
'''
if h is not None: self.h = h
if a is not None: self.a = a
if gs is not None: self.gs = gs
if nimgs is not None: self.nimgs = nimgs
if ew_eta is not None: self.ew_eta = ew_eta
if ew_cut is not None: self.ew_cut = ew_cut
if pseudo is not None: self.pseudo = pseudo
if basis is not None: self.basis = basis
if dimension is not None: self.dimension = dimension
if precision is not None: self.precision = precision
if rcut is not None: self.rcut = rcut
if ecp is not None: self.ecp = ecp
assert (self.a is not None)
assert (self.gs is not None or self.ke_cutoff is not None)
if 'unit' in kwargs:
self.unit = kwargs['unit']
if 'atom' in kwargs:
self.atom = kwargs['atom']
# Set-up pseudopotential if it exists
# This must happen before build() because it affects
# tot_electrons() via atom_charge()
self.ecp, self.pseudo = classify_ecp_pseudo(self, self.ecp,
self.pseudo)
if self.pseudo is not None:
if isinstance(self.pseudo, str):
# specify global pseudo for whole molecule
_atom = self.format_atom(self.atom, unit=self.unit)
uniq_atoms = set([a[0] for a in _atom])
self._pseudo = self.format_pseudo(
dict([(a, self.pseudo) for a in uniq_atoms]))
else:
self._pseudo = self.format_pseudo(self.pseudo)
# Do regular Mole.build with usual kwargs
_built = self._built
mole.Mole.build(self, False, parse_arg, *args, **kwargs)
if self.rcut is None:
self.rcut = max(
[self.bas_rcut(ib, self.precision) for ib in range(self.nbas)])
_a = self.lattice_vectors()
if np.linalg.det(_a) < 0 and self.dimension == 3:
sys.stderr.write('''WARNING!
Lattice are not in right-handed coordinate system. This can cause wrong value for some integrals.
It's recommended to resort the lattice vectors to\na = %s\n\n''' %
_a[[0, 2, 1]])
if self.gs is None:
assert (self.ke_cutoff is not None)
self.gs = pbctools.cutoff_to_gs(_a, self.ke_cutoff)
if self.ew_eta is None or self.ew_cut is None:
self.ew_eta, self.ew_cut = self.get_ewald_params(
self.precision, self.gs)
if dump_input and not _built and self.verbose > logger.NOTE:
self.dump_input()
logger.info(self, 'lattice vectors a1 [%.9f, %.9f, %.9f]', *_a[0])
logger.info(self, ' a2 [%.9f, %.9f, %.9f]', *_a[1])
logger.info(self, ' a3 [%.9f, %.9f, %.9f]', *_a[2])
logger.info(self, 'dimension = %s', self.dimension)
logger.info(self, 'Cell volume = %g', self.vol)
logger.info(self, 'rcut = %s (nimgs = %s)', self.rcut, self.nimgs)
logger.info(self, 'lattice sum = %d cells',
len(self.get_lattice_Ls()))
logger.info(self, 'precision = %g', self.precision)
logger.info(self, 'gs (FFT-mesh) = %s', self.gs)
logger.info(self, 'pseudo = %s', self.pseudo)
logger.info(self, 'ke_cutoff = %s', self.ke_cutoff)
logger.info(self, 'ew_eta = %g', self.ew_eta)
logger.info(self, 'ew_cut = %s (nimgs = %s)', self.ew_cut,
self.get_bounding_sphere(self.ew_cut))
return self
def build(self, dump_input=True, parse_arg=True,
h=None, gs=None, ke_cutoff=None, precision=None, nimgs=None,
ew_eta=None, ew_cut=None, pseudo=None, basis=None,
dimension=None,
*args, **kwargs):
'''Setup Mole molecule and Cell and initialize some control parameters.
Whenever you change the value of the attributes of :class:`Cell`,
you need call this function to refresh the internal data of Cell.
Kwargs:
h : (3,3) ndarray
The real-space unit cell lattice vectors, a "three-column" array [a1|a2|a3]
gs : (3,) ndarray of ints
The number of *positive* G-vectors along each direction.
pseudo : dict or str
To define pseudopotential. If given, overwrite :attr:`Cell.pseudo`
'''
if h is not None: self.h = h
if gs is not None: self.gs = gs
if nimgs is not None: self.nimgs = nimgs
if ew_eta is not None: self.ew_eta = ew_eta
if ew_cut is not None: self.ew_cut = ew_cut
if pseudo is not None: self.pseudo = pseudo
if basis is not None: self.basis = basis
if dimension is not None: self.dimension = dimension
assert(self.h is not None)
assert(self.gs is not None or self.ke_cutoff is not None)
if 'unit' in kwargs:
self.unit = kwargs['unit']
if 'atom' in kwargs:
self.atom = kwargs['atom']
# Set-up pseudopotential if it exists
# This must happen before build() because it affects
# tot_electrons() via atom_charge()
if self.pseudo is not None:
if isinstance(self.pseudo, str):
# specify global pseudo for whole molecule
_atom = self.format_atom(self.atom, unit=self.unit)
uniq_atoms = set([a[0] for a in _atom])
self._pseudo = self.format_pseudo(dict([(a, self.pseudo)
for a in uniq_atoms]))
else:
self._pseudo = self.format_pseudo(self.pseudo)
# Do regular Mole.build with usual kwargs
_built = self._built
mole.Mole.build(self, False, parse_arg, *args, **kwargs)
self._h = self.lattice_vectors()
self.vol = float(scipy.linalg.det(self._h))
if self.nimgs is None:
self.nimgs = self.get_nimgs(self.precision)
if self.gs is None:
assert(self.ke_cutoff is not None)
self.gs = pbctools.cutoff_to_gs(self._h, self.ke_cutoff)
if self.ew_eta is None or self.ew_cut is None:
self.ew_eta, self.ew_cut = self.get_ewald_params(self.precision, self.gs)
if dump_input and not _built and self.verbose > logger.NOTE:
self.dump_input()
logger.info(self, 'lattice vector [a1 | a2 | a3 ]')
logger.info(self, ' [%.9f | %.9f | %.9f]', *self._h[0])
logger.info(self, ' [%.9f | %.9f | %.9f]', *self._h[1])
logger.info(self, ' [%.9f | %.9f | %.9f]', *self._h[2])
logger.info(self, 'Cell volume = %g', self.vol)
logger.info(self, 'nimgs = %s lattice sum = %d cells',
self.nimgs, len(self.get_lattice_Ls(self.nimgs)))
logger.info(self, 'precision = %g', self.precision)
logger.info(self, 'gs (grid size) = %s', self.gs)
logger.info(self, 'pseudo = %s', self.pseudo)
logger.info(self, 'ke_cutoff = %s', self.ke_cutoff)
logger.info(self, 'ew_eta = %g', self.ew_eta)
logger.info(self, 'ew_cut = %s', self.ew_cut)
return self
def build(self, dump_input=True, parse_arg=True,
h=None, gs=None, ke_cutoff=None, precision=None, nimgs=None,
ew_eta=None, ew_cut=None, pseudo=None, basis=None,
dimension=None,
*args, **kwargs):
'''Setup Mole molecule and Cell and initialize some control parameters.
Whenever you change the value of the attributes of :class:`Cell`,
you need call this function to refresh the internal data of Cell.
Kwargs:
h : (3,3) ndarray
The real-space unit cell lattice vectors, a "three-column" array [a1|a2|a3]
gs : (3,) ndarray of ints
The number of *positive* G-vectors along each direction.
pseudo : dict or str
To define pseudopotential. If given, overwrite :attr:`Cell.pseudo`
'''
if h is not None: self.h = h
if gs is not None: self.gs = gs
if nimgs is not None: self.nimgs = nimgs
if ew_eta is not None: self.ew_eta = ew_eta
if ew_cut is not None: self.ew_cut = ew_cut
if pseudo is not None: self.pseudo = pseudo
if basis is not None: self.basis = basis
if dimension is not None: self.dimension = dimension
assert(self.h is not None)
assert(self.gs is not None or self.ke_cutoff is not None)
if 'unit' in kwargs:
self.unit = kwargs['unit']
if 'atom' in kwargs:
self.atom = kwargs['atom']
# Set-up pseudopotential if it exists
# This must happen before build() because it affects
# tot_electrons() via atom_charge()
if self.pseudo is not None:
if isinstance(self.pseudo, str):
# specify global pseudo for whole molecule
_atom = self.format_atom(self.atom, unit=self.unit)
uniq_atoms = set([a[0] for a in _atom])
self._pseudo = self.format_pseudo(dict([(a, self.pseudo)
for a in uniq_atoms]))
else:
self._pseudo = self.format_pseudo(self.pseudo)
# Do regular Mole.build with usual kwargs
_built = self._built
mole.Mole.build(self, False, parse_arg, *args, **kwargs)
self._h = self.lattice_vectors()
self.vol = float(scipy.linalg.det(self._h))
if self.nimgs is None:
self.nimgs = self.get_nimgs(self.precision)
if self.gs is None:
assert(self.ke_cutoff is not None)
self.gs = pbctools.cutoff_to_gs(self._h, self.ke_cutoff)
if self.ew_eta is None or self.ew_cut is None:
self.ew_eta, self.ew_cut = self.get_ewald_params(self.precision, self.gs)
if dump_input and not _built and self.verbose > logger.NOTE:
self.dump_input()
logger.info(self, 'lattice vector [a1 | a2 | a3 ]')
logger.info(self, ' [%.9f | %.9f | %.9f]', *self._h[0])
logger.info(self, ' [%.9f | %.9f | %.9f]', *self._h[1])
logger.info(self, ' [%.9f | %.9f | %.9f]', *self._h[2])
logger.info(self, 'Cell volume = %g', self.vol)
logger.info(self, 'nimgs = %s lattice sum = %d cells',
self.nimgs, len(self.get_lattice_Ls(self.nimgs)))
logger.info(self, 'precision = %g', self.precision)
logger.info(self, 'gs (grid size) = %s', self.gs)
logger.info(self, 'pseudo = %s', self.pseudo)
logger.info(self, 'ke_cutoff = %s', self.ke_cutoff)
logger.info(self, 'ew_eta = %g', self.ew_eta)
logger.info(self, 'ew_cut = %s', self.ew_cut)
return self
def build(self, dump_input=True, parse_arg=True,
a=None, gs=None, ke_cutoff=None, precision=None, nimgs=None,
ew_eta=None, ew_cut=None, pseudo=None, basis=None, h=None,
dimension=None, rcut= None, ecp=None,
*args, **kwargs):
'''Setup Mole molecule and Cell and initialize some control parameters.
Whenever you change the value of the attributes of :class:`Cell`,
you need call this function to refresh the internal data of Cell.
Kwargs:
a : (3,3) ndarray
The real-space unit cell lattice vectors. Each row represents
a lattice vector.
gs : (3,) ndarray of ints
The number of *positive* G-vectors along each direction.
pseudo : dict or str
To define pseudopotential. If given, overwrite :attr:`Cell.pseudo`
'''
if h is not None: self.h = h
if a is not None: self.a = a
if gs is not None: self.gs = gs
if nimgs is not None: self.nimgs = nimgs
if ew_eta is not None: self.ew_eta = ew_eta
if ew_cut is not None: self.ew_cut = ew_cut
if pseudo is not None: self.pseudo = pseudo
if basis is not None: self.basis = basis
if dimension is not None: self.dimension = dimension
if precision is not None: self.precision = precision
if rcut is not None: self.rcut = rcut
if ecp is not None: self.ecp = ecp
assert(self.a is not None)
assert(self.gs is not None or self.ke_cutoff is not None)
if 'unit' in kwargs:
self.unit = kwargs['unit']
if 'atom' in kwargs:
self.atom = kwargs['atom']
# Set-up pseudopotential if it exists
# This must happen before build() because it affects
# tot_electrons() via atom_charge()
self.ecp, self.pseudo = classify_ecp_pseudo(self, self.ecp, self.pseudo)
if self.pseudo is not None:
if isinstance(self.pseudo, str):
# specify global pseudo for whole molecule
_atom = self.format_atom(self.atom, unit=self.unit)
uniq_atoms = set([a[0] for a in _atom])
self._pseudo = self.format_pseudo(dict([(a, self.pseudo)
for a in uniq_atoms]))
else:
self._pseudo = self.format_pseudo(self.pseudo)
# Do regular Mole.build with usual kwargs
_built = self._built
mole.Mole.build(self, False, parse_arg, *args, **kwargs)
if self.rcut is None:
self.rcut = max([self.bas_rcut(ib, self.precision)
for ib in range(self.nbas)])
_a = self.lattice_vectors()
if self.gs is None:
assert(self.ke_cutoff is not None)
self.gs = pbctools.cutoff_to_gs(_a, self.ke_cutoff)
if self.ew_eta is None or self.ew_cut is None:
self.ew_eta, self.ew_cut = self.get_ewald_params(self.precision, self.gs)
if dump_input and not _built and self.verbose > logger.NOTE:
self.dump_input()
logger.info(self, 'lattice vectors a1 [%.9f, %.9f, %.9f]', *_a[0])
logger.info(self, ' a2 [%.9f, %.9f, %.9f]', *_a[1])
logger.info(self, ' a3 [%.9f, %.9f, %.9f]', *_a[2])
logger.info(self, 'dimension = %s', self.dimension)
logger.info(self, 'Cell volume = %g', self.vol)
logger.info(self, 'rcut = %s (nimgs = %s)', self.rcut, self.nimgs)
logger.info(self, 'lattice sum = %d cells', len(self.get_lattice_Ls()))
logger.info(self, 'precision = %g', self.precision)
logger.info(self, 'gs (FFT-mesh) = %s', self.gs)
logger.info(self, 'pseudo = %s', self.pseudo)
logger.info(self, 'ke_cutoff = %s', self.ke_cutoff)
logger.info(self, 'ew_eta = %g', self.ew_eta)
logger.info(self, 'ew_cut = %s (nimgs = %s)', self.ew_cut,
self.get_bounding_sphere(self.ew_cut))
return self