def test_hessian_full_water(): ff = get_ff_water() hessian = estimate_cart_hessian(ff) assert hessian.shape == (9, 9) evals = np.linalg.eigvalsh(hessian) print(evals) assert sum(abs(evals) < 1e-10) == 3
def test_CN_online_blind(): # Setup a test FF and run simulation without any HDF5 file ff = get_ff_water() ff.update_rvecs(np.diag([20., 20., 20.])) select0 = ff.system.get_indexes('O') select1 = ff.system.get_indexes('H') rdf = RDF(4.5*angstrom, 0.1*angstrom, select0=select0, select1=select1) nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=rdf) nve.run(5) assert nve.counter == 5 assert rdf.nsample == 6 assert (rdf.CN[:7] == 0).all() assert (np.round(rdf.CN[-7:], decimals=5) == 2).all()
def test_basic_water(): nve = VerletIntegrator(get_ff_water(), 1.0 * femtosecond) nve.run(5) assert nve.counter == 5
def test_basic_water(): nve = VerletIntegrator(get_ff_water(), 1.0*femtosecond) nve.run(5) assert nve.counter == 5