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_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