def recv_multiplicity(self, multiplicity=None):
""" Receive the electronic multiplicity through MDI
Arguments:
multiplicity: New multiplicity of the system. If None, receive through MDI.
"""
if multiplicity is None:
multiplicity = MDI_Recv(1, MDI_INT, self.comm)
self.molecule.set_multiplicity(multiplicity)
def recv_total_charge(self, charge=None):
""" Receive the total system charge through MDI
Arguments:
charge: New charge of the system. If None, receive through MDI.
"""
if charge is None:
charge = MDI_Recv(1, MDI_DOUBLE, self.comm)
self.molecule.set_molecular_charge(int(round(charge)))
def recv_lattice(self, lattice=None):
""" Receive the charges of a set of lattice point charges through MDI
Arguments:
lattice: New charges of the lattice of point charges. If None, receive through MDI.
"""
if lattice is None:
self.lattice = MDI_Recv(self.nlattice, MDI_DOUBLE, self.comm)
else:
self.lattice = lattice
self.set_lattice_field()
def recv_coords(self, coords=None):
""" Receive a set of nuclear coordinates through MDI and assign them to the atoms in the current molecule
Arguments:
coords: New nuclear coordinates. If None, receive through MDI.
"""
natom = self.molecule.natom()
if coords is None:
coords = MDI_Recv(3 * natom, MDI_DOUBLE, self.comm)
matrix = psi4.core.Matrix.from_array(np.array(coords).reshape(-1, 3))
self.molecule.set_geometry(matrix)
def recv_clattice(self, clattice=None):
""" Receive the coordinates of a set of lattice point charges through MDI
Arguments:
clattice: New coordinates of the lattice of point charges. If None, receive through MDI.
"""
if clattice is None:
self.clattice = MDI_Recv(3 * self.nlattice, MDI_DOUBLE, self.comm)
else:
self.clattice = clattice
self.set_lattice_field()
def recv_masses(self, masses: Optional[List[float]] = None) -> None:
"""Receive a set of nuclear masses through MDI and assign them to the atoms in the current molecule
Parameters
----------
masses : :obj:`list` of :obj:`float`, optional
New nuclear masses. If None, receive through MDI.
"""
natom = len(self.molecule.geometry)
if masses is None:
masses = MDI_Recv(natom, MDI_DOUBLE, self.comm)
self.update_molecule("masses", masses)
def recv_nlattice(self, nlattice=None):
""" Receive the number of lattice point charges through MDI
Arguments:
nlattice: New number of point charges. If None, receive through MDI.
"""
if nlattice is None:
self.nlattice = MDI_Recv(1, MDI_INT, self.comm)
else:
self.nlattice = nlattice
self.clattice = [0.0 for ilat in range(3 * self.nlattice)]
self.lattice = [0.0 for ilat in range(self.nlattice)]
self.set_lattice_field()
def recv_multiplicity(self, multiplicity: Optional[int] = None) -> None:
"""Receive the electronic multiplicity through MDI
Parameters
----------
multiplicity : int, optional
New multiplicity of the system. If None, receive through MDI.
"""
if multiplicity is None:
multiplicity = MDI_Recv(1, MDI_INT, self.comm)
self.multiplicity = multiplicity
# Allow a validation error here, because a future >TOTCHARGE command might resolve it
try:
self.update_molecule("molecular_multiplicity", self.multiplicity)
except qcel.exceptions.ValidationError:
pass
def recv_total_charge(self, charge: Optional[float] = None) -> None:
"""Receive the total system charge through MDI
Parameters
----------
charge : float, optional
New charge of the system. If None, receive through MDI.
"""
if charge is None:
charge = MDI_Recv(1, MDI_DOUBLE, self.comm)
self.total_charge = charge
# Allow a validation error here, because a future >ELEC_MULT command might resolve it
try:
self.update_molecule("molecular_charge", self.total_charge)
except qcel.exceptions.ValidationError:
pass
def recv_elements(self, elements: Optional[List[int]] = None):
"""Receive a set of atomic numbers through MDI and assign them to the atoms in the current molecule
Parameters
----------
elements : :obj:`list` of :obj:`int`, optional
New element numbers. If None, receive through MDI.
"""
natom = len(self.molecule.geometry)
if elements is None:
elements = MDI_Recv(natom, MDI_INT, self.comm)
for iatom in range(natom):
self.molecule.symbols[iatom] = qcel.periodictable.to_symbol(
elements[iatom])
return elements
def recv_coords(self, coords: Optional[np.ndarray] = None) -> None:
""" Receive a set of nuclear coordinates through MDI and assign them to the atoms in the current molecule
Parameters
----------
coords : np.ndarray, optional
New nuclear coordinates. If None, receive through MDI.
"""
natom = len(self.molecule.geometry)
if coords is None:
coords = MDI_Recv(3 * natom, MDI_DOUBLE_NUMPY, self.comm)
new_geometry = np.reshape(coords, (-1, 3))
self.molecule = qcel.models.Molecule(**{
**self.molecule.dict(),
**{
"geometry": new_geometry
}
})
def recv_masses(self, masses=None):
""" Receive a set of nuclear masses through MDI and assign them to the atoms in the current molecule
Arguments:
masses: New nuclear masses. If None, receive through MDI.
"""
natom = self.molecule.natom()
if masses is None:
masses = MDI_Recv(natom, MDI_DOUBLE, self.comm)
# Assign the mass of all atoms, taking care to avoid ghost atoms
jatom = 0
for iatom in range(natom):
while self.molecule.fZ(jatom) == 0 and jatom < self.molecule.nallatom():
jatom = jatom + 1
if jatom >= self.molecule.nallatom():
raise Exception('Unexpected number of ghost atoms when receiving masses')
self.molecule.set_mass(iatom, masses[jatom])
jatom = jatom + 1
