def __init__(self, coordinates, numbers, pseudo_numbers, density, grid, scheme="h", **kwargs):
wpart = wpart_schemes[scheme]
# make proatom database
if scheme.lower() not in ["mbis", "b"]:
if "proatomdb" not in kwargs.keys():
proatomdb = ProAtomDB.from_refatoms(numbers)
kwargs["proatomdb"] = proatomdb
# partition
self.part = wpart(coordinates, numbers, pseudo_numbers, grid, density, **kwargs)
self.part.do_all()
self.grid = grid
self.density = density
self.coordines = coordinates
self.numbers = numbers
self.pseudo_numbers = pseudo_numbers
self.charges = self.part['charges']
def __init__(self,
coordinates,
numbers,
pseudo_numbers,
density,
grid,
scheme="h",
**kwargs):
"""Initialize class.
Parameters
----------
coordinates : np.ndarray, shape=(M, 3)
Cartesian coordinates of `M` atoms in the molecule.
numbers : np.ndarray, shape=(M,)
Atomic number of `M` atoms in the molecule.
pseudo_numbers : np.ndarray, shape=(M,)
Pseudo-number of `M` atoms in the molecule.
density : np.ndarray, shape=(N,)
Total density to be partitioned.
grid : BeckeMolGrid
Instance of BeckeMolGrid numerical integration grid.
scheme : str
Type of atoms-in-molecule partitioning scheme.
"""
wpart = wpart_schemes[scheme]
# make proatom database
if scheme.lower() not in ["mbis", "b"]:
if "proatomdb" not in kwargs.keys():
proatomdb = ProAtomDB.from_refatoms(numbers)
kwargs["proatomdb"] = proatomdb
kwargs["local"] = False
# partition
self.part = wpart(coordinates, numbers, pseudo_numbers, grid, density,
**kwargs)
self.part.do_charges()
self.grid = grid
self.density = density
self.coordines = coordinates
self.numbers = numbers
self.pseudo_numbers = pseudo_numbers
self.charges = self.part['charges']
def get_dict_population(molecule, approach, scheme, **kwargs):
r"""Return dictionary of number of electrons and corresponding atomic charges values.
Parameters
----------
molecule : Molecule or Sequence of Molecule
Instance of Molecule class, or sequence of Molecule class instances.
approach : str, optional
Choose between "FMR" (fragment of molecular response) or "RMF"
(response of molecular fragment).
scheme : str
Partitioning scheme.
kwargs : optional
"""
# check approach
if approach.lower() not in ["rmf", "fmr"]:
raise ValueError("Argument approach={0} is not valid.".format(approach))
# case of populations available in molecule
if scheme.lower() not in wpart_schemes:
# check approach & molecule instances
if approach.lower() != "rmf":
raise ValueError("Condensing with scheme={0} is only possible in combination with "
"approach='RMF'! Given approach={1}".format(scheme, approach))
if (not hasattr(type(molecule), "__iter__") or len(molecule) != 3 or not
np.all([isinstance(mol, Molecule) for mol in molecule])):
raise ValueError("Condensing with scheme={0} needs 3 molecules!".format(scheme))
# get populations
pops = [getattr(mol, scheme + "_charges") for mol in molecule]
if np.any([isinstance(pop, type(None)) for pop in pops]):
raise ValueError("Condensing scheme={0} is not possible, because attribute {1}_charges "
"of molecule instances is 'None'.".format(scheme, scheme.lower()))
# make dictionary of populations
dict_pops = dict([(sum(m.mo.nelectrons), m.numbers - pop) for m, pop in zip(molecule, pops)])
return dict_pops
# case of condensing the density using denspart
try:
# check whether molecules have the same coordinates
get_matching_attr(molecule, "coordinates", 1.e-4)
same_coordinates = True
except ValueError:
if approach.lower() == "fmr":
raise ValueError("When geometries of molecules are different, only approach='RMF' "
"is possible! Given approach={0}".format(approach.upper()))
same_coordinates = False
# find reference molecule
if isinstance(molecule, Molecule):
mol0 = molecule
elif np.all([isinstance(mol, Molecule) for mol in molecule]):
if len(molecule) != 3:
raise ValueError("Condensing within FD approach, currently works for "
"only 3 molecules! Given {0} molecules.".format(len(molecule)))
# reference molecule is the middle molecule (for 3 molecules)
dict_mols = {sum(mol.mo.nelectrons): mol for mol in molecule}
mol0 = dict_mols.pop(sorted(dict_mols.keys())[1])
else:
raise ValueError("Argument molecule not recognized!")
# check and generate partitioning class & proatomdb
wpart = wpart_schemes[scheme]
# make proatom database
if scheme.lower() not in ["mbis", "b"]:
if "proatomdb" not in list(kwargs.keys()) or kwargs["proatomdb"] is None:
proatomdb = ProAtomDB.from_refatoms(mol0.numbers)
kwargs["proatomdb"] = proatomdb
# check or generate molecular grid
grid = get_molecular_grid(molecule, kwargs.pop("grid", None))
# compute dictionary of number of electron and density
dict_dens = get_dict_density(molecule, grid.points)
# compute population of reference molecule
part0 = wpart(mol0.coordinates, mol0.numbers, mol0.pseudo_numbers, grid,
dict_dens[sum(mol0.mo.nelectrons)], **kwargs)
part0.do_all()
# record population of reference system
dict_pops = dict([(sum(mol0.mo.nelectrons), part0["populations"])])
del dict_dens[sum(mol0.mo.nelectrons)]
# compute and record populations given grid in a dictionary
for nelec, dens in dict_dens.items():
if approach.lower() == "fmr":
# fragment of molecular response
pops = condense_to_atoms(dens, part0)
elif approach.lower() == "rmf":
# response of molecular fragment
if not same_coordinates:
mol = dict_mols[nelec]
grid = get_molecular_grid(molecule, None)
dens = molecule.compute_density(grid.points, "ab", None)
else:
mol = mol0
parts = wpart(mol.coordinates, mol.numbers, mol.pseudo_numbers,
grid, dens, **kwargs)
parts.do_all()
pops = parts["populations"]
else:
raise ValueError("Condensing approach {0} is not recognized!".format(approach))
# Store number of electron and populations in a dictionary
dict_pops[nelec] = pops
return dict_pops