def prepare_sapt_molecule(sapt_dimer: core.Molecule, sapt_basis: str) -> Tuple[core.Molecule, core.Molecule, core.Molecule]:
"""
Prepares a dimer molecule for a SAPT computations. Returns the dimer, monomerA, and monomerB.
"""
# Shifting to C1 so we need to copy the active molecule
sapt_dimer = sapt_dimer.clone()
if sapt_dimer.schoenflies_symbol() != 'c1':
core.print_out(' SAPT does not make use of molecular symmetry, further calculations in C1 point group.\n')
sapt_dimer.reset_point_group('c1')
sapt_dimer.fix_orientation(True)
sapt_dimer.fix_com(True)
sapt_dimer.update_geometry()
else:
sapt_dimer.update_geometry() # make sure since mol from wfn, kwarg, or P::e
sapt_dimer.fix_orientation(True)
sapt_dimer.fix_com(True)
nfrag = sapt_dimer.nfragments()
if nfrag == 3:
# Midbond case
if sapt_basis == 'monomer':
raise ValidationError("SAPT basis cannot both be monomer centered and have midbond functions.")
midbond = sapt_dimer.extract_subsets(3)
ztotal = 0
for n in range(midbond.natom()):
ztotal += midbond.Z(n)
if ztotal > 0:
raise ValidationError("SAPT third monomer must be a midbond function (all ghosts).")
ghosts = ([2, 3], [1, 3])
elif nfrag == 2:
# Classical dimer case
ghosts = (2, 1)
else:
raise ValidationError('SAPT requires active molecule to have 2 fragments, not %s.' % (nfrag))
if sapt_basis == 'dimer':
monomerA = sapt_dimer.extract_subsets(1, ghosts[0])
monomerA.set_name('monomerA')
monomerB = sapt_dimer.extract_subsets(2, ghosts[1])
monomerB.set_name('monomerB')
elif sapt_basis == 'monomer':
monomerA = sapt_dimer.extract_subsets(1)
monomerA.set_name('monomerA')
monomerB = sapt_dimer.extract_subsets(2)
monomerB.set_name('monomerB')
else:
raise ValidationError("SAPT basis %s not recognized" % sapt_basis)
return (sapt_dimer, monomerA, monomerB)
def compute_hessian(self,
molecule: core.Molecule,
wfn: core.Wavefunction = None) -> core.Matrix:
"""Compute dispersion Hessian based on engine, dispersion level, and parameters in `self`.
Uses finite difference, as no dispersion engine has analytic second derivatives.
Parameters
----------
molecule
System for which to compute empirical dispersion correction.
wfn
Location to set QCVariables
Returns
-------
Matrix
(3*nat, 3*nat) dispersion Hessian [Eh/a0/a0].
"""
optstash = p4util.OptionsState(['PRINT'], ['PARENT_SYMMETRY'])
core.set_global_option('PRINT', 0)
core.print_out(
"\n\n Analytical Dispersion Hessians are not supported by dftd3 or gcp.\n"
)
core.print_out(
" Computing the Hessian through finite difference of gradients.\n\n"
)
# Setup the molecule
molclone = molecule.clone()
molclone.reinterpret_coordentry(False)
molclone.fix_orientation(True)
molclone.fix_com(True)
# Record undisplaced symmetry for projection of diplaced point groups
core.set_global_option("PARENT_SYMMETRY",
molecule.schoenflies_symbol())
findif_meta_dict = driver_findif.hessian_from_gradients_geometries(
molclone, -1)
for displacement in findif_meta_dict["displacements"].values():
geom_array = np.reshape(displacement["geometry"], (-1, 3))
molclone.set_geometry(core.Matrix.from_array(geom_array))
molclone.update_geometry()
displacement["gradient"] = self.compute_gradient(
molclone).np.ravel().tolist()
H = driver_findif.assemble_hessian_from_gradients(findif_meta_dict, -1)
if wfn is not None:
wfn.set_variable('DISPERSION CORRECTION HESSIAN', H)
optstash.restore()
return core.Matrix.from_array(H)