def psi4mol_to_cppemol(psi4mol):
mol = cppe.Molecule()
geom = psi4mol.geometry().np
for i, c in enumerate(geom):
a = cppe.Atom((int(psi4mol.Z(i))), *c)
mol.append(a)
return mol
def _create_cppe_state(self, mol):
cppe_mol = cppe.Molecule()
for z, coord in zip(mol.atom_charges(), mol.atom_coords()):
cppe_mol.append(cppe.Atom(z, *coord))
def callback(output):
logger.info(self, output)
cppe_state = cppe.CppeState(self.options, cppe_mol, callback)
cppe_state.calculate_static_energies_and_fields()
return cppe_state
def molecule(self):
"""
The HF data a testcase is based upon
"""
ret = {}
for k in self.testcases:
datafile = fullfile(k + ".hdf5")
f = h5py.File(datafile, 'r')
mol = cppe.Molecule()
for z, coord in zip(f['atom_charges'], f['atom_coords']):
mol.append(cppe.Atom(z, *coord))
ret[k] = mol
return ret
def grad_nuclear_field_fdiff(atoms, coords, potentials, step_au=1e-3):
"""
Computes the finite difference gradient
with a 5-point stencil
"""
natoms = len(atoms)
polsites = cppe.get_polarizable_sites(potentials)
grad = np.zeros((natoms, 3, len(polsites), 3))
for i in range(natoms):
for c in range(3):
print("Computing dE/d{} for atom {}.".format(coords_label[c], i))
for f, p in zip(*stencils["5p"]):
coords_p = coords.copy()
coords_p[i, c] += f * step_au
mol_p = cppe.Molecule()
for z, coord in zip(atoms, coords_p):
mol_p.append(cppe.Atom(z, *coord))
nf = NuclearFields(mol_p, potentials)
en_pert = nf.compute().reshape(len(polsites), 3)
grad[i, c] += p * en_pert / step_au
return grad
def grad_nuclear_interaction_energy_fdiff(atoms,
coords,
potentials,
step_au=1e-3):
"""
Computes the finite difference gradient
with a 5-point stencil
"""
natoms = len(atoms)
grad = np.zeros((natoms, 3))
for i in range(natoms):
for c in range(3):
print("Computing dE/d{} for atom {}.".format(coords_label[c], i))
for f, p in zip(*stencils["5p"]):
coords_p = coords.copy()
coords_p[i, c] += f * step_au
mol_p = cppe.Molecule()
for z, coord in zip(atoms, coords_p):
mol_p.append(cppe.Atom(z, *coord))
mexp = MultipoleExpansion(mol_p, potentials)
en_pert = mexp.interaction_energy()
grad[i, c] += p * en_pert / step_au
return grad
