def test_input_ecp(self):
mol1 = gto.Mole()
mol1.atom = mol0.atom
mol1.ecp = 'lanl2dz'
mol1.build(False, False)
gto.basis.load_ecp('lanl08', 'O')
gto.format_ecp({'O': 'lanl08', 1: 'lanl2dz'})
self.assertRaises(KeyError, gto.format_ecp, {'H': 'lan2ldz'})
def test_input_ecp(self):
mol1 = gto.Mole()
mol1.atom = mol0.atom
mol1.ecp = 'lanl2dz'
mol1.build(False, False)
gto.basis.load_ecp('lanl08', 'O')
gto.format_ecp({'O':'lanl08', 1:'lanl2dz'})
self.assertRaises(KeyError, gto.format_ecp, {'H':'lan2ldz'})
def concat_mols(mol_list):
"""Concatenates Mole objects into one Mole.
Parameters
----------
mol_list : list
List of Mole objects to concatenate into single Mole.
"""
assert (len(mol_list) > 1), "Must have more than 1 mol object"
total_spin = 0
for i, mol_obj in enumerate(mol_list):
mol1 = gto.mole.copy(mol_obj)
total_spin += mol1.spin
mol1.unit = 'bohr'
atom_coords = mol1.atom_coords()
mol1.atom = []
uniq_atoms = set()
for j, coord in enumerate(atom_coords):
a_symb = mol1.atom_symbol(j) + '-' + str(i)
uniq_atoms.add(a_symb)
mol1.atom.append([a_symb, tuple(coord)])
if isinstance(mol1.basis, (str, tuple, list)):
new_basis = dict(((a, mol1.basis) for a in uniq_atoms))
elif isinstance(mol1.basis, dict):
old_basis = copy.copy(mol1.basis)
new_basis = {}
if 'default' in old_basis:
default_basis = old_basis['default']
new_basis = dict(((a, default_basis) for a in uniq_atoms))
del old_basis['default']
for atom_symb in old_basis:
new_symb = atom_symb + '-' + str(i)
new_basis[new_symb] = old_basis[atom_symb]
else:
new_basis = mol1.basis
mol1.basis = gto.format_basis(new_basis)
if mol1.ecp:
if isinstance(mol1.ecp, str):
new_ecp = dict(((a, str(mol1.ecp)) for a in uniq_atoms))
elif isinstance(mol1.ecp, dict):
old_ecp = copy.copy(mol1.ecp)
if 'default' in old_ecp:
default_ecp = old_ecp['default']
new_ecp = dict(((a, default_ecp) for a in uniq_atoms))
del old_ecp['default']
for atom_symb in old_ecp:
new_symb = atom_symb + '-' + str(i)
new_ecp[new_symb] = old_ecp[atom_symb]
else:
new_ecp = mol1.ecp
mol1.ecp = gto.format_ecp(new_ecp)
mol1.build()
if i == 0:
mol2 = gto.mole.copy(mol1)
else:
new_mol = gto.mole.conc_mol(mol2, mol1)
new_mol.build()
mol2 = new_mol
conc_mol = mol2
conc_mol.spin = total_spin #check that this works properly.
#Remove overlapping ghost atoms.
final_mol = __remove_overlap_ghost(conc_mol)
final_mol = conc_mol
return final_mol