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_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)