def base_multipole_fields(self, options):
mol = cache.molecule["pna"]
cppe_state = CppeState(options, mol, lambda s: None)
cppe_state.calculate_static_energies_and_fields()
multipole_fields = cppe_state.multipole_fields
potentials = cppe_state.potentials
polsites = get_polarizable_sites(potentials)
ref = np.zeros((len(potentials), 3))
for i, p1 in enumerate(polsites):
for j, p2 in enumerate(polsites):
if not p1.is_polarizable:
continue
if p1.index == p2.index:
continue
if p1.excludes_site(p2.index):
continue
diff = p1.position - p2.position
for m in p2.multipoles:
M_full = symmetry.unfold_tensor(m.values, m.k)
if options.get("damp_multipole", False):
a_i = p1.polarizability.isotropic_value
a_j = p2.polarizability.isotropic_value
damp = cppe_state.options["damping_factor_multipole"]
a = 1/(a_i*a_j)**(1/6) * damp
ref[p1.index, :] += polfields.thole_exp_field(
diff, m.k, M_full, 1, a)
else:
ref[p1.index, :] += polfields.field(
diff, m.k, M_full, 1)
np.testing.assert_allclose(ref.flatten(), multipole_fields, atol=1e-14)
def test_nuclear_fields(self):
mol = cache.molecule["pna"]
options = {"potfile": self.potfile_path}
cppe_state = CppeState(options, mol, lambda s: None)
cppe_state.calculate_static_energies_and_fields()
nuclear_fields = cppe_state.nuclear_fields
potentials = cppe_state.potentials
ref = np.zeros((len(potentials), 3))
for i, p in enumerate(potentials):
for a in mol:
diff = p.position - a.position
ref[i, :] += a.charge * diff / np.linalg.norm(diff)**3
np.testing.assert_allclose(ref.flatten(), nuclear_fields, atol=1e-14)
def test_solver_by_inversion(self):
mol = cache.molecule["pna"]
options = {"potfile": self.potfile_path,
"induced_thresh": 1e-12}
cppe_state = CppeState(options, mol, print_callback)
cppe_state.calculate_static_energies_and_fields()
static_fields = cppe_state.static_fields
zeros = np.zeros_like(static_fields)
cppe_state.update_induced_moments(zeros, False)
potentials = cppe_state.potentials
polsites = get_polarizable_sites(potentials)
npolsites = cppe_state.get_polarizable_site_number()
bmat = np.zeros((3 * npolsites, 3 * npolsites))
for s1, pot1 in enumerate(polsites):
pol = pot1.polarizability
inv_alpha = triangle_to_mat(pol.values)
bmat[block(s1, s1)] = np.linalg.inv(inv_alpha)
for s2, pot2 in enumerate(polsites):
if pot1.excludes_site(pot2.index) or s1 == s2:
continue
diff = pot2.position - pot1.position
T12 = T_recursive(2, diff)
if s1 > s2:
bmat[block(s1, s2)] = -triangle_to_mat(T12)
bmat[block(s2, s1)] = -triangle_to_mat(T12)
# Test the matrix apply
bmatrix_cpp = BMatrix(polsites, options)
ret = bmatrix_cpp.compute_apply(static_fields)
ret_ref = bmat @ static_fields
np.testing.assert_allclose(ret, ret_ref, atol=1e-12)
ret1 = bmatrix_cpp.compute_apply_slice(static_fields, 0, 8)
ret2 = bmatrix_cpp.compute_apply_slice(static_fields, 8, npolsites)
ret_all = ret1 + ret2
np.testing.assert_allclose(ret_all, ret_ref, atol=1e-12)
# build the Bmatrix from C++
A = LinearOperator(2 * (static_fields.size,),
matvec=bmatrix_cpp.compute_apply)
Afull = A @ np.eye(static_fields.size)
np.testing.assert_allclose(Afull, bmat, atol=1e-20)
induced_moments_direct = np.linalg.inv(bmat) @ static_fields
induced_moments_solver = cppe_state.get_induced_moments()
np.testing.assert_almost_equal(induced_moments_solver,
induced_moments_direct, decimal=9)
ind_mom = InducedMoments(potentials, options)
res_cg = ind_mom.compute_cg(static_fields)
np.testing.assert_allclose(res_cg, induced_moments_direct, atol=1e-10)
binv = bmatrix_cpp.direct_inverse()
np.testing.assert_allclose(binv @ static_fields,
induced_moments_direct, atol=1e-15)
def test_set_all(self):
custom_options = {
"potfile": self.potfile_path,
"iso_pol": True,
"induced_thresh": 1e-4,
"maxiter": 500,
"damp_induced": True,
"damp_multipole": True,
"damping_factor_induced": 213.04,
"damping_factor_multipole": 213.04,
# summation
"summation_induced_fields": "fmm",
"tree_expansion_order": 4,
"tree_ncrit": 12,
"theta": 0.2,
# border
"pe_border": True,
"border_type": "redist",
"border_rmin": 2.6,
"border_nredist": 2,
"border_redist_order": 2,
"border_redist_pol": True,
}
cppe_state = CppeState(custom_options)
for k in custom_options:
assert custom_options[k] == cppe_state.options[k]
def solve_induced_moments(options, mol):
cppe_state = CppeState(options, mol)
cppe_state.calculate_static_energies_and_fields()
static_fields = np.array(cppe_state.get_static_fields())
zeros = np.zeros_like(static_fields)
cppe_state.update_induced_moments(zeros, False)
return cppe_state
def test_defaults(self):
options_dict = {"potfile": self.potfile_path}
cppe_state = CppeState(options_dict)
defaults = self.default_options.copy()
defaults.pop("potfile")
cppe_options = cppe_state.options.copy()
cppe_options.pop("potfile")
assert len(defaults) == len(cppe_options)
for k in defaults:
assert defaults[k] == cppe_state.options[k]
def test_solver_by_inversion(self):
f = h5py.File(self.pna_path, 'r')
mol = Molecule()
options = PeOptions()
options.potfile = self.potfile_path
options.induced_thresh = 12
for z, coord in zip(f['atom_charges'], f['atom_coords']):
mol.append(Atom(z, *coord))
cppe_state = CppeState(options, mol)
cppe_state.calculate_static_energies_and_fields()
static_fields = np.array(cppe_state.get_static_fields())
zeros = np.zeros_like(static_fields)
cppe_state.update_induced_moments(zeros, False)
potentials = cppe_state.get_potentials()
polsites = get_polarizable_sites(potentials)
npolsites = cppe_state.get_polarizable_site_number()
bmat = np.zeros((3 * npolsites, 3 * npolsites))
coeffs = Tk_coefficients(5)
for s1, pot1 in enumerate(polsites):
for pol in pot1.get_polarizabilities():
inv_alpha = triangle_to_mat(pol.get_values())
bmat[block(s1, s1)] = np.linalg.inv(inv_alpha)
for s2, pot2 in enumerate(polsites):
if pot1.excludes_site(pot2.index) or s1 == s2:
continue
diff = pot2.get_site_position() - pot1.get_site_position()
T12 = Tk_tensor(2, diff, coeffs)
if s1 > s2:
bmat[block(s1, s2)] = -triangle_to_mat(T12)
bmat[block(s2, s1)] = -triangle_to_mat(T12)
induced_moments_direct = np.linalg.inv(bmat) @ static_fields
induced_moments_solver = cppe_state.get_induced_moments()
np.testing.assert_almost_equal(induced_moments_solver,
induced_moments_direct, decimal=10)
def solve_induced_moments(options, mol):
cppe_state = CppeState(options, mol, print_callback)
cppe_state.calculate_static_energies_and_fields()
static_fields = cppe_state.static_fields
np.testing.assert_allclose(
static_fields, cppe_state.nuclear_fields + cppe_state.multipole_fields
)
zeros = np.zeros_like(static_fields)
cppe_state.update_induced_moments(zeros, False)
return cppe_state
def test_compute_nuclear_interaction_energy(self):
f = h5py.File(self.pna_path, 'r')
mol = Molecule()
options = PeOptions()
options.potfile = self.potfile_path
for z, coord in zip(f['atom_charges'], f['atom_coords']):
mol.append(Atom(z, *coord))
cppe_state = CppeState(options, mol)
assert cppe_state.get_polarizable_site_number() == 18
cppe_state.calculate_static_energies_and_fields()
en_el_nuc = cppe_state.get_energies().get("Electrostatic/Nuclear")
ref = -0.321349401430 # pelib
np.testing.assert_almost_equal(en_el_nuc, ref, decimal=9)
def test_compute_nuclear_interaction_energy(self):
mol = cache.molecule["pna"]
options = {"potfile": self.potfile_path}
cppe_state = CppeState(options, mol, print_callback)
assert cppe_state.get_polarizable_site_number() == 18
cppe_state.calculate_static_energies_and_fields()
en_el_nuc = cppe_state.energies["Electrostatic"]["Nuclear"]
ref = -0.321349401430 # pelib
np.testing.assert_almost_equal(en_el_nuc, ref, decimal=9)
# TODO: split these tests up, use cache
# test writing to the energy container from Python
bla = cppe_state.energies["Electrostatic"]
bla["Nuclear"] = -10.0
assert bla["Nuclear"] == -10.0
cppe_state.energies["Electrostatic"]["Nuclear"] = -20.0
assert cppe_state.energies["Electrostatic"]["Nuclear"] == -20.0
cppe_state.energies["Electrostatic"]["Electronic"] = 1.0
cppe_state.energies["Electrostatic"]["Nuclear"] = 2.0
cppe_state.energies["Electrostatic"]["Multipoles"] = 3.0
cppe_state.energies["Polarization"]["Electronic"] = 4.0
cppe_state.energies["Polarization"]["Nuclear"] = 5.0
cppe_state.energies["Polarization"]["Multipole"] = 6.0
total_energy = (
cppe_state.energies["Electrostatic"]["Electronic"]
+ cppe_state.energies["Electrostatic"]["Nuclear"]
+ cppe_state.energies["Electrostatic"]["Multipoles"]
+ cppe_state.energies["Polarization"]["Electronic"]
+ cppe_state.energies["Polarization"]["Nuclear"]
+ cppe_state.energies["Polarization"]["Multipole"]
)
assert cppe_state.total_energy == total_energy
def test_invalid_key(self):
defaults = self.default_options.copy()
defaults["invalid_key"] = 42
with pytest.raises(ValueError):
CppeState(defaults)