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)
def compute_gradient(self,
molecule: core.Molecule,
wfn: core.Wavefunction = None) -> core.Matrix:
"""Compute dispersion gradient based on engine, dispersion level, and parameters in `self`.
Parameters
----------
molecule
System for which to compute empirical dispersion correction.
wfn
Location to set QCVariables
Returns
-------
Matrix
(nat, 3) dispersion gradient [Eh/a0].
"""
if self.engine in ['dftd3', 'mp2d']:
resi = AtomicInput(
**{
'driver': 'gradient',
'model': {
'method': self.fctldash,
'basis': '(auto)',
},
'keywords': {
'level_hint': self.dashlevel,
'params_tweaks': self.dashparams,
'dashcoeff_supplement': self.dashcoeff_supplement,
'verbose': 1,
},
'molecule': molecule.to_schema(dtype=2),
'provenance': p4util.provenance_stamp(__name__),
})
jobrec = qcng.compute(
resi,
self.engine,
raise_error=True,
local_options={"scratch_directory": core.IOManager.shared_object().get_default_path()})
dashd_part = core.Matrix.from_array(jobrec.extras['qcvars']['DISPERSION CORRECTION GRADIENT'])
if wfn is not None:
for k, qca in jobrec.extras['qcvars'].items():
if "CURRENT" not in k:
wfn.set_variable(k, float(qca) if isinstance(qca, str) else qca)
if self.fctldash in ['hf3c', 'pbeh3c']:
jobrec = qcng.compute(
resi,
"gcp",
raise_error=True,
local_options={"scratch_directory": core.IOManager.shared_object().get_default_path()})
gcp_part = core.Matrix.from_array(jobrec.return_result)
dashd_part.add(gcp_part)
return dashd_part
else:
return self.disp.compute_gradient(molecule)
def makepsi4(atomcoords, atomnos, charge=0, mult=1):
"""Create a Psi4 Molecule."""
_check_psi4(_found_psi4)
return Molecule.from_arrays(
name="notitle",
elez=atomnos,
geom=atomcoords,
units="Angstrom",
molecular_charge=charge,
molecular_multiplicity=mult,
)
def auto_fragments(molecule: core.Molecule = None, seed_atoms: List = None) -> core.Molecule:
r"""Detects fragments in unfragmented molecule using BFS algorithm.
Currently only used for the WebMO implementation of SAPT.
Parameters
----------
molecule : :ref:`molecule <op_py_molecule>`, optional
The target molecule, if not the last molecule defined.
seed_atoms
List of lists of atoms (0-indexed) belonging to independent fragments.
Useful to prompt algorithm or to define intramolecular fragments through
border atoms. Example: `[[1, 0], [2]]`
Returns
-------
:py:class:`~psi4.core.Molecule` |w--w| fragmented molecule in
Cartesian, fixed-geom (no variable values), no dummy-atom format.
Examples
--------
>>> # [1] prepare unfragmented (and non-adjacent-atom) HHFF into (HF)_2 molecule ready for SAPT
>>> molecule mol {\nH 0.0 0.0 0.0\nH 2.0 0.0 0.0\nF 0.0 1.0 0.0\nF 2.0 1.0 0.0\n}
>>> print mol.nfragments() # 1
>>> fragmol = auto_fragments()
>>> print fragmol.nfragments() # 2
"""
# Make sure the molecule the user provided is the active one
if molecule is None:
molecule = core.get_active_molecule()
molecule.update_geometry()
molname = molecule.name()
frag, bmol = molecule.BFS(seed_atoms=seed_atoms, return_molecule=True)
bmol.set_name(molname)
bmol.print_cluster()
core.print_out(""" Exiting auto_fragments\n""")
return bmol
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_energy(self,
molecule: core.Molecule,
wfn: core.Wavefunction = None) -> float:
"""Compute dispersion energy based on engine, dispersion level, and parameters in `self`.
Parameters
----------
molecule
System for which to compute empirical dispersion correction.
wfn
Location to set QCVariables
Returns
-------
float
Dispersion energy [Eh].
Notes
-----
:psivar:`DISPERSION CORRECTION ENERGY`
Disp always set. Overridden in SCF finalization, but that only changes for "-3C" methods.
:psivar:`fctl DISPERSION CORRECTION ENERGY`
Set if :py:attr:`fctldash` nonempty.
"""
if self.engine in ['dftd3', 'mp2d']:
resi = AtomicInput(
**{
'driver': 'energy',
'model': {
'method': self.fctldash,
'basis': '(auto)',
},
'keywords': {
'level_hint': self.dashlevel,
'params_tweaks': self.dashparams,
'dashcoeff_supplement': self.dashcoeff_supplement,
'pair_resolved': self.save_pairwise_disp,
'verbose': 1,
},
'molecule': molecule.to_schema(dtype=2),
'provenance': p4util.provenance_stamp(__name__),
})
jobrec = qcng.compute(
resi,
self.engine,
raise_error=True,
local_options={
"scratch_directory":
core.IOManager.shared_object().get_default_path()
})
dashd_part = float(
jobrec.extras['qcvars']['DISPERSION CORRECTION ENERGY'])
if wfn is not None:
for k, qca in jobrec.extras['qcvars'].items():
wfn.set_variable(
k,
float(qca) if isinstance(qca, str) else qca)
# Pass along the pairwise dispersion decomposition if we need it
if self.save_pairwise_disp is True:
wfn.set_variable(
"PAIRWISE DISPERSION CORRECTION ANALYSIS",
jobrec.extras['qcvars']
["2-BODY PAIRWISE DISPERSION CORRECTION ANALYSIS"])
if self.fctldash in ['hf3c', 'pbeh3c']:
jobrec = qcng.compute(
resi,
"gcp",
raise_error=True,
local_options={
"scratch_directory":
core.IOManager.shared_object().get_default_path()
})
gcp_part = jobrec.return_result
dashd_part += gcp_part
return dashd_part
else:
ene = self.disp.compute_energy(molecule)
core.set_variable('DISPERSION CORRECTION ENERGY', ene)
if self.fctldash:
core.set_variable(
f"{self.fctldash} DISPERSION CORRECTION ENERGY", ene)
return ene