def get_forces(self, atoms, coords):
xyz = make_xyz_str(atoms, coords.reshape(-1, 3) * BOHR2ANG)
mol = psi4.geometry(xyz)
energy, wfn = psi4.energy(self.meth_bas, return_wfn=True)
gradient = psi4.gradient(self.meth_bas, molecule=mol, ref_wfn=wfn)
results = {
"energy": energy,
"forces": -np.asarray(gradient).flatten(),
}
return results
def write_trj(self, path, prefix, coords=None):
path = pathlib.Path(path)
atoms = self.geometry.atoms
if coords is None:
coords = self.all_mw_coords
coords = coords.copy()
coords /= self.m_sqrt
coords = coords.reshape(-1, len(atoms), 3) * BOHR2ANG
# all_mw_coords = self.all_mw_coords.flatten()
trj_string = make_trj_str(atoms, coords, comments=self.all_energies)
trj_fn = f"{prefix}_irc.trj"
with open(path / trj_fn, "w") as handle:
handle.write(trj_string)
first_coords = coords[0]
first_fn = f"{prefix}_first.xyz"
with open(path / first_fn, "w") as handle:
handle.write(make_xyz_str(atoms, first_coords))
last_coords = coords[-1]
first_fn = f"{prefix}_last.xyz"
with open(path / first_fn, "w") as handle:
handle.write(make_xyz_str(atoms, last_coords))
def as_xyz(self, comment=""):
"""Current geometry as a string in XYZ-format.
Parameters
----------
comment : str, optional
Will be written in the second line (comment line) of the
XYZ-string.
Returns
-------
xyz_str : str
Current geometry as string in XYZ-format.
"""
coords = self._coords * BOHR2ANG
if comment == "":
comment = self.comment
return make_xyz_str(self.atoms, coords.reshape((-1, 3)), comment)
def prepare_coords(self, atoms, coords):
coords = coords * BOHR2ANG
return make_xyz_str(atoms, coords.reshape((-1, 3)))