def get_energy(self,coords,multiplicity,state,runtype=None):
if self.hasRanForCurrentCoords==False or (coords != self.currentCoords).any():
self.currentCoords = coords.copy()
geom = manage_xyz.np_to_xyz(self.geom,self.currentCoords)
self.runall(geom,runtype)
Energy = self.Energies[(multiplicity,state)]
if Energy.unit=="Hartree":
return Energy.value*units.KCAL_MOL_PER_AU
elif Energy.unit=='kcal/mol':
return Energy.value
elif Energy.unit==None:
return Energy.value
def get_coupling(self,coords,multiplicity,state1,state2,frozen_atoms=None):
if self.hasRanForCurrentCoords==False or (coords != self.currentCoords).any():
self.currentCoords = coords.copy()
geom = manage_xyz.np_to_xyz(self.geom,self.currentCoords)
self.runall(geom)
Coupling = self.Couplings[(state1,state2)]
if Coupling.value is not None:
if frozen_atoms is not None:
for a in [3*i for i in frozen_atoms]:
Coupling.value[a:a+3,0]=0.
if Coupling.unit=="Hartree/Bohr":
return Coupling.value *units.ANGSTROM_TO_AU #Ha/bohr*bohr/ang=Ha/ang
else:
raise NotImplementedError
else:
return None
def get_gradient(self,coords,multiplicity,state,frozen_atoms=None):
if self.hasRanForCurrentCoords==False or (coords != self.currentCoords).any():
self.currentCoords = coords.copy()
geom = manage_xyz.np_to_xyz(self.geom,self.currentCoords)
self.runall(geom)
Gradient = self.Gradients[(multiplicity,state)]
if Gradient.value is not None:
if frozen_atoms is not None:
for a in frozen_atoms:
Gradient.value[a, :]= 0.
if Gradient.unit=="Hartree/Bohr":
return Gradient.value *units.ANGSTROM_TO_AU #Ha/bohr*bohr/ang=Ha/ang
elif Gradient.unit=="kcal/mol/Angstrom":
return Gradient.value *units.KCAL_MOL_TO_AU #kcalmol/A*Ha/kcalmol=Ha/ang
else:
raise NotImplementedError
else:
return None
def eckart_frame(
geom,
masses,
):
""" Moves the molecule to the Eckart frame
Params:
geom ((natoms,4) np.ndarray) - Contains atom symbol and xyz coordinates
masses ((natoms) np.ndarray) - Atom masses
Returns:
COM ((3), np.ndarray) - Molecule center of mess
L ((3), np.ndarray) - Principal moments
O ((3,3), np.ndarray)- Principle axes of inertial tensor
geom2 ((natoms,4 np.ndarray) - Contains new geometry (atom symbol and xyz coordinates)
"""
# Center of mass
COM = np.sum(manage_xyz.xyz_to_np(geom) * np.outer(masses, [1.0] * 3),
0) / np.sum(masses)
# Inertial tensor
I = np.zeros((3, 3))
for atom, mass in zip(geom, masses):
I[0, 0] += mass * (atom[1] - COM[0]) * (atom[1] - COM[0])
I[0, 1] += mass * (atom[1] - COM[0]) * (atom[2] - COM[1])
I[0, 2] += mass * (atom[1] - COM[0]) * (atom[3] - COM[2])
I[1, 0] += mass * (atom[2] - COM[1]) * (atom[1] - COM[0])
I[1, 1] += mass * (atom[2] - COM[1]) * (atom[2] - COM[1])
I[1, 2] += mass * (atom[2] - COM[1]) * (atom[3] - COM[2])
I[2, 0] += mass * (atom[3] - COM[2]) * (atom[1] - COM[0])
I[2, 1] += mass * (atom[3] - COM[2]) * (atom[2] - COM[1])
I[2, 2] += mass * (atom[3] - COM[2]) * (atom[3] - COM[2])
I /= np.sum(masses)
# Principal moments/Principle axes of inertial tensor
L, O = np.linalg.eigh(I)
# Eckart geometry
geom2 = manage_xyz.np_to_xyz(
geom,
np.dot((manage_xyz.xyz_to_np(geom) - np.outer(np.ones(
(len(masses), )), COM)), O))
return COM, L, O, geom2
def copy_from_options(MoleculeA,
xyz=None,
fnm=None,
new_node_id=1,
copy_wavefunction=True):
"""Create a copy of MoleculeA"""
print(" Copying from MoleculA {}".format(MoleculeA.node_id))
PES = type(MoleculeA.PES).create_pes_from(
PES=MoleculeA.PES, options={'node_id': new_node_id})
if xyz is not None:
new_geom = manage_xyz.np_to_xyz(MoleculeA.geometry, xyz)
coord_obj = type(MoleculeA.coord_obj)(
MoleculeA.coord_obj.options.copy().set_values({"xyz": xyz}))
elif fnm is not None:
new_geom = manage_xyz.read_xyz(fnm, scale=1.)
xyz = manage_xyz.xyz_to_np(new_geom)
coord_obj = type(MoleculeA.coord_obj)(
MoleculeA.coord_obj.options.copy().set_values({"xyz": xyz}))
else:
new_geom = MoleculeA.geometry
coord_obj = type(MoleculeA.coord_obj)(
MoleculeA.coord_obj.options.copy())
return Molecule(MoleculeA.Data.copy().set_values({
'PES':
PES,
'coord_obj':
coord_obj,
'geom':
new_geom,
'node_id':
new_node_id,
'copy_wavefunction':
copy_wavefunction,
}))