def __init__(self, atoms, basis=None):
self.atomtypes = mole.atom_types(atoms, basis)
# fake systems, which treates the atoms of different basis as different atoms.
# the fake systems do not have the same symmetry as the potential
# it's only used to determine the main (Z-)axis
chg1 = numpy.pi - 2
coords = []
fake_chgs = []
idx = []
for k, lst in self.atomtypes.items():
idx.append(lst)
coords.append([atoms[i][1] for i in lst])
ksymb = mole._rm_digit(k)
if ksymb != k or ksymb == 'GHOST':
fake_chgs.append([chg1] * len(lst))
chg1 *= numpy.pi-2
else:
fake_chgs.append([mole._charge(ksymb)] * len(lst))
coords = numpy.array(numpy.vstack(coords), dtype=float)
fake_chgs = numpy.hstack(fake_chgs)
self.charge_center = numpy.einsum('i,ij->j', fake_chgs, coords)/fake_chgs.sum()
coords = coords - self.charge_center
self.im = numpy.einsum('i,ij,ik->jk', fake_chgs, coords, coords)/fake_chgs.sum()
idx = numpy.argsort(numpy.hstack(idx))
self.atoms = numpy.hstack((fake_chgs.reshape(-1,1), coords))[idx]
def format_basis(basis_tab):
"""Convert the input :attr:`Cell.basis` to the internal data format.
``{ atom: (l, kappa, ((-exp, c_1, c_2, ..), nprim, nctr, ptr-exps, ptr-contraction-coeff)), ... }``
Args:
basis_tab : list
Similar to :attr:`Cell.basis`, it **cannot** be a str
Returns:
Formated :attr:`~Cell.basis`
Examples:
>>> pbc.format_basis({'H':'gth-szv'})
{'H': [[0,
(8.3744350009, -0.0283380461),
(1.8058681460, -0.1333810052),
(0.4852528328, -0.3995676063),
(0.1658236932, -0.5531027541)]]}
"""
fmt_basis = {}
for atom in basis_tab.keys():
symb = _symbol(atom)
rawsymb = _rm_digit(symb)
stdsymb = _std_symbol(rawsymb)
symb = symb.replace(rawsymb, stdsymb)
if isinstance(basis_tab[atom], str):
fmt_basis[symb] = basis.load(basis_tab[atom], stdsymb)
else:
fmt_basis[symb] = basis_tab[atom]
return fmt_basis
def __init__(self, atoms, basis=None):
self.atomtypes = mole.atom_types(atoms, basis)
# fake systems, which treates the atoms of different basis as different atoms.
# the fake systems do not have the same symmetry as the potential
# it's only used to determine the main (Z-)axis
chg1 = numpy.pi - 2
coords = []
fake_chgs = []
idx = []
for k, lst in self.atomtypes.items():
idx.append(lst)
coords.append([atoms[i][1] for i in lst])
ksymb = mole._rm_digit(k)
if ksymb != k or ksymb == 'GHOST':
# Put random charges on the decorated atoms
fake_chgs.append([chg1] * len(lst))
chg1 *= numpy.pi-2
else:
fake_chgs.append([mole._charge(ksymb)] * len(lst))
coords = numpy.array(numpy.vstack(coords), dtype=float)
fake_chgs = numpy.hstack(fake_chgs)
self.charge_center = numpy.einsum('i,ij->j', fake_chgs, coords)/fake_chgs.sum()
coords = coords - self.charge_center
self.im = numpy.einsum('i,ij,ik->jk', fake_chgs, coords, coords)/fake_chgs.sum()
idx = numpy.argsort(numpy.hstack(idx))
self.atoms = numpy.hstack((fake_chgs.reshape(-1,1), coords))[idx]
def _basis_offset_for_atoms(atoms, basis_tab):
basoff = [0]
n = 0
for at in atoms:
symb = mole._symbol(at[0])
if symb in basis_tab:
bas0 = basis_tab[symb]
else:
bas0 = basis_tab[mole._rm_digit(symb)]
for b in bas0:
angl = b[0]
n += _num_contract(b) * (angl * 2 + 1)
basoff.append(n)
return n, basoff
def __init__(self, atoms, basis=None):
self.atomtypes = mole.atom_types(atoms, basis)
# fake systems, which treates the atoms of different basis as different atoms.
# the fake systems do not have the same symmetry as the potential
# it's only used to determine the main (Z-)axis
chg1 = numpy.pi - 2
coords = []
fake_chgs = []
idx = []
for k, lst in self.atomtypes.items():
idx.append(lst)
coords.append([atoms[i][1] for i in lst])
ksymb = mole._rm_digit(k)
if ksymb != k:
# Put random charges on the decorated atoms
fake_chgs.append([chg1] * len(lst))
chg1 *= numpy.pi - 2
elif mole.is_ghost_atom(k):
if ksymb == 'X' or ksymb.upper() == 'GHOST':
fake_chgs.append([.3] * len(lst))
elif ksymb[0] == 'X':
fake_chgs.append([mole.charge(ksymb[1:]) + .3] * len(lst))
elif ksymb[:5] == 'GHOST':
fake_chgs.append([mole.charge(ksymb[5:]) + .3] * len(lst))
else:
fake_chgs.append([mole.charge(ksymb)] * len(lst))
coords = numpy.array(numpy.vstack(coords), dtype=float)
fake_chgs = numpy.hstack(fake_chgs)
self.charge_center = numpy.einsum('i,ij->j', fake_chgs,
coords) / fake_chgs.sum()
coords = coords - self.charge_center
idx = numpy.argsort(numpy.hstack(idx))
self.atoms = numpy.hstack((fake_chgs.reshape(-1, 1), coords))[idx]
self.group_atoms_by_distance = []
decimals = int(-numpy.log10(TOLERANCE)) - 1
for index in self.atomtypes.values():
index = numpy.asarray(index)
c = self.atoms[index, 1:]
dists = numpy.around(norm(c, axis=1), decimals)
u, idx = numpy.unique(dists, return_inverse=True)
for i, s in enumerate(u):
self.group_atoms_by_distance.append(index[idx == i])
def __init__(self, atoms, basis=None):
self.atomtypes = mole.atom_types(atoms, basis)
# fake systems, which treates the atoms of different basis as different atoms.
# the fake systems do not have the same symmetry as the potential
# it's only used to determine the main (Z-)axis
chg1 = numpy.pi - 2
coords = []
fake_chgs = []
idx = []
for k, lst in self.atomtypes.items():
idx.append(lst)
coords.append([atoms[i][1] for i in lst])
ksymb = mole._rm_digit(k)
if ksymb != k:
# Put random charges on the decorated atoms
fake_chgs.append([chg1] * len(lst))
chg1 *= numpy.pi-2
elif mole.is_ghost_atom(k):
if ksymb == 'X' or ksymb.upper() == 'GHOST':
fake_chgs.append([.3] * len(lst))
elif ksymb[0] == 'X':
fake_chgs.append([mole.charge(ksymb[1:])+.3] * len(lst))
elif ksymb[:5] == 'GHOST':
fake_chgs.append([mole.charge(ksymb[5:])+.3] * len(lst))
else:
fake_chgs.append([mole.charge(ksymb)] * len(lst))
coords = numpy.array(numpy.vstack(coords), dtype=float)
fake_chgs = numpy.hstack(fake_chgs)
self.charge_center = numpy.einsum('i,ij->j', fake_chgs, coords)/fake_chgs.sum()
coords = coords - self.charge_center
idx = numpy.argsort(numpy.hstack(idx))
self.atoms = numpy.hstack((fake_chgs.reshape(-1,1), coords))[idx]
self.group_atoms_by_distance = []
decimals = int(-numpy.log10(TOLERANCE)) - 1
for index in self.atomtypes.values():
index = numpy.asarray(index)
c = self.atoms[index,1:]
dists = numpy.around(norm(c, axis=1), decimals)
u, idx = numpy.unique(dists, return_inverse=True)
for i, s in enumerate(u):
self.group_atoms_by_distance.append(index[idx == i])
def format_pseudo(pseudo_tab):
r'''Convert the input :attr:`Cell.pseudo` (dict) to the internal data format::
{ atom: ( (nelec_s, nele_p, nelec_d, ...),
rloc, nexp, (cexp_1, cexp_2, ..., cexp_nexp),
nproj_types,
(r1, nproj1, ( (hproj1[1,1], hproj1[1,2], ..., hproj1[1,nproj1]),
(hproj1[2,1], hproj1[2,2], ..., hproj1[2,nproj1]),
...
(hproj1[nproj1,1], hproj1[nproj1,2], ... ) )),
(r2, nproj2, ( (hproj2[1,1], hproj2[1,2], ..., hproj2[1,nproj1]),
... ) )
)
... }
Args:
pseudo_tab : dict
Similar to :attr:`Cell.pseudo` (a dict), it **cannot** be a str
Returns:
Formatted :attr:`~Cell.pseudo`
Examples:
>>> pbc.format_pseudo({'H':'gth-blyp', 'He': 'gth-pade'})
{'H': [[1],
0.2, 2, [-4.19596147, 0.73049821], 0],
'He': [[2],
0.2, 2, [-9.1120234, 1.69836797], 0]}
'''
fmt_pseudo = {}
for atom in pseudo_tab:
symb = _symbol(atom)
rawsymb = _rm_digit(symb)
stdsymb = _std_symbol(rawsymb)
symb = symb.replace(rawsymb, stdsymb)
if isinstance(pseudo_tab[atom], str):
fmt_pseudo[symb] = pseudo.load(pseudo_tab[atom], stdsymb)
else:
fmt_pseudo[symb] = pseudo_tab[atom]
return fmt_pseudo
def format_pseudo(pseudo_tab):
'''Convert the input :attr:`Cell.pseudo` (dict) to the internal data format.
``{ atom: ( (nelec_s, nele_p, nelec_d, ...),
rloc, nexp, (cexp_1, cexp_2, ..., cexp_nexp),
nproj_types,
(r1, nproj1, ( (hproj1[1,1], hproj1[1,2], ..., hproj1[1,nproj1]),
(hproj1[2,1], hproj1[2,2], ..., hproj1[2,nproj1]),
...
(hproj1[nproj1,1], hproj1[nproj1,2], ... ) )),
(r2, nproj2, ( (hproj2[1,1], hproj2[1,2], ..., hproj2[1,nproj1]),
... ) )
)
... }``
Args:
pseudo_tab : dict
Similar to :attr:`Cell.pseudo` (a dict), it **cannot** be a str
Returns:
Formatted :attr:`~Cell.pseudo`
Examples:
>>> pbc.format_pseudo({'H':'gth-blyp', 'He': 'gth-pade'})
{'H': [[1],
0.2, 2, [-4.19596147, 0.73049821], 0],
'He': [[2],
0.2, 2, [-9.1120234, 1.69836797], 0]}
'''
fmt_pseudo = {}
for atom in pseudo_tab.keys():
symb = _symbol(atom)
rawsymb = _rm_digit(symb)
stdsymb = _std_symbol(rawsymb)
symb = symb.replace(rawsymb, stdsymb)
if isinstance(pseudo_tab[atom], str):
fmt_pseudo[symb] = pseudo.load(pseudo_tab[atom], stdsymb)
else:
fmt_pseudo[symb] = pseudo_tab[atom]
return fmt_pseudo
