def basis_subset2(symbols, largebasis='dzp', smallbasis='sz'):
"""Same as basis_subset, but for an entire list of atoms."""
largebasis = types2atomtypes(symbols, largebasis, default='dzp')
smallbasis = types2atomtypes(symbols, smallbasis, default='sz')
mask = []
for symbol, large, small in zip(symbols, largebasis, smallbasis):
mask.extend(basis_subset(symbol, large, small))
return np.asarray(mask, bool)
def basis_subset2(symbols, largebasis='dzp', smallbasis='sz'):
"""Same as basis_subset, but for an entire list of atoms."""
largebasis = types2atomtypes(symbols, largebasis, default='dzp')
smallbasis = types2atomtypes(symbols, smallbasis, default='sz')
mask = []
for symbol, large, small in zip(symbols, largebasis, smallbasis):
mask.extend(basis_subset(symbol, large, small))
return np.asarray(mask, bool)
def get_bfi2(symbols, basis, a_list):
"""Same as get_bfi, but does not require an LCAO calc"""
basis = types2atomtypes(symbols, basis, default='dzp')
bfs_list = []
i = 0
for a, symbol in enumerate(symbols):
nao = Basis(symbol, basis[a]).nao
if a in a_list:
bfs_list += range(i, i + nao)
i += nao
return bfs_list
def get_bfi2(symbols, basis, a_list):
"""Same as get_bfi, but does not require an LCAO calc"""
basis = types2atomtypes(symbols, basis, default='dzp')
bfs_list = []
i = 0
for a, symbol in enumerate(symbols):
nao = Basis(symbol, basis[a]).nao
if a in a_list:
bfs_list += range(i, i + nao)
i += nao
return bfs_list
def get_bf_centers(atoms, basis=None):
calc = atoms.get_calculator()
if calc is None or isinstance(calc, SinglePointCalculator):
symbols = atoms.get_chemical_symbols()
basis_a = types2atomtypes(symbols, basis, 'dzp')
nao_a = [Basis(symbol, type).nao
for symbol, type in zip(symbols, basis_a)]
else:
if not calc.initialized:
calc.initialize(atoms)
nao_a = [calc.wfs.setups[a].nao for a in range(len(atoms))]
pos_ic = []
for pos, nao in zip(atoms.get_positions(), nao_a):
pos_ic.extend(pos[None].repeat(nao, 0))
return np.array(pos_ic)
def get_bf_centers(atoms, basis=None):
calc = atoms.get_calculator()
if calc is None or isinstance(calc, SinglePointCalculator):
symbols = atoms.get_chemical_symbols()
basis_a = types2atomtypes(symbols, basis, 'dzp')
nao_a = [Basis(symbol, type).nao
for symbol, type in zip(symbols, basis_a)]
else:
if not calc.initialized:
calc.initialize(atoms)
nao_a = [calc.wfs.setups[a].nao for a in range(len(atoms))]
pos_ic = []
for pos, nao in zip(atoms.get_positions(), nao_a):
pos_ic.extend(pos[None].repeat(nao, 0))
return np.array(pos_ic)
def get_bfs_atoms(atoms, basis=None, default='dzp', method='extend'):
"""Get ba
atoms - ase::atoms
basis - dict of elements with correspondig basis set type
default - str
"""
if basis is None:
basis = {symbol:default for symbol in set(atoms.symbols)}
symbols = atoms.get_chemical_symbols()
basis_a = types2atomtypes(symbols, basis, default)
nao_a = [Basis(symbol, type).nao
for symbol, type in zip(symbols, basis_a)]
Mvalues = []
Mattr = getattr(Mvalues, method)
i0 = 0
for nao in nao_a:
i1 = i0 + nao
Mattr(list(range(i0,i1)))
i0 = i1
return Mvalues
