def test_sim_dyn_save_hdf5(setup_cte_sim, mocker):
'''Test that the dynamics solution is saved a loaded correctly'''
with temp_bin_filename() as temp_filename:
mocked = mocker.patch('simetuc.odesolver._solve_ode')
# the num_states changes when the temp lattice is created,
# allocate 2x so that we're safe. Also make the num_points 1000.
mocked.return_value = np.random.random(
(1000, 2 * setup_cte_sim.states['energy_states']))
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_dynamics()
assert mocked.call_count == 2
with temp_bin_filename() as filename:
solution.save(filename)
sol_hdf5 = simulations.DynamicsSolution.load(filename)
assert sol_hdf5
assert sol_hdf5.cte == solution.cte
assert np.allclose(sol_hdf5.y_sol, solution.y_sol)
assert np.allclose(sol_hdf5.t_sol, solution.t_sol)
assert sol_hdf5.index_S_i == solution.index_S_i
assert sol_hdf5.index_A_j == solution.index_A_j
assert sol_hdf5 == solution
sol_hdf5.log_errors()
sol_hdf5.plot()
plotter.plt.close('all')
def test_sim_conc_dep_dyn(setup_cte_sim, mocker):
'''Test that the concentration dependence works'''
with temp_bin_filename() as temp_filename:
mocked = mocker.patch('simetuc.odesolver._solve_ode')
# the num_states changes when the temp lattice is created,
# allocate 2x so that we're safe. Also make the num_points 1000.
mocked.return_value = np.random.random(
(1000, 2 * setup_cte_sim['states']['energy_states']))
conc_list = [(0, 0.3), (0.1, 0.3), (0.1, 0)]
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_concentration_dependence(conc_list,
dynamics=True)
# dynamics call solve_ode twice (pulse and relaxation)
assert mocked.call_count == 2 * len(conc_list)
assert solution
solution.plot()
solution.log_errors()
with temp_config_filename('') as filename:
solution.save(filename)
sol_hdf5 = simulations.ConcentrationDependenceSolution.load(filename)
assert sol_hdf5
assert sol_hdf5 == solution
sol_hdf5.plot()
plotter.plt.close('all')
def test_sim_power_dep_no_plot(setup_cte_sim, mocker):
'''A plot was requested, but no_plot is set'''
setup_cte_sim['no_plot'] = True
with temp_bin_filename() as temp_filename:
mocked = mocker.patch(
'simetuc.simulations.Simulations.simulate_pulsed_steady_state')
mocked.return_value = simulations.SteadyStateSolution(
np.empty((1000, )),
np.empty((1000, 2 * setup_cte_sim['states']['energy_states'])), [],
[], setup_cte_sim)
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
power_dens_list = np.logspace(1, 2, 3)
solution = sim.simulate_power_dependence(power_dens_list)
assert mocked.call_count == len(power_dens_list)
with pytest.warns(plotter.PlotWarning) as warnings:
solution.plot()
# assert len(warnings) == 1 # one warning
warning = warnings.pop(plotter.PlotWarning)
assert issubclass(warning.category, plotter.PlotWarning)
assert 'A plot was requested, but no_plot setting is set' in str(
warning.message)
plotter.plt.close('all')
def test_sim_steady2(setup_cte_sim):
'''Test average steady state'''
setup_cte_sim['excitations']['Vis_473'][0].t_pulse = 1e-08
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_avg_steady_state()
assert solution
def test_sim_conc_dep_no_plot(setup_cte_sim, mocker):
'''A plot was requested, but no_plot is set'''
setup_cte_sim['no_plot'] = True
with temp_bin_filename() as temp_filename:
mocked = mocker.patch('simetuc.odesolver._solve_ode')
# the num_states changes when the temp lattice is created,
# allocate 2x so that we're safe. Also make the num_points 1000.
mocked.return_value = np.random.random(
(1000, 2 * setup_cte_sim['states']['energy_states']))
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
conc_list = [(0.01, 0.3), (0.1, 0.3)]
solution = sim.simulate_concentration_dependence(conc_list,
dynamics=False)
assert mocked.call_count == 2 * len(conc_list)
with pytest.warns(plotter.PlotWarning) as warnings:
solution.plot()
# assert len(warnings) == 1 # one warning
warning = warnings.pop(plotter.PlotWarning)
assert issubclass(warning.category, plotter.PlotWarning)
assert 'A plot was requested, but no_plot setting is set' in str(
warning.message)
plotter.plt.close('all')
def test_sim_dyn_no_t_pulse(setup_cte_sim):
'''Test that the dynamics gives an error if t_pulse is not defined'''
del setup_cte_sim['excitations']['Vis_473'][0].t_pulse
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
with pytest.raises(AttributeError):
sim.simulate_dynamics()
def test_sim_dyn_save_txt(setup_cte_sim):
'''Test that the dynamics solution is saved a loaded correctly'''
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_dynamics()
with temp_config_filename('') as filename:
solution.save_txt(filename)
def test_sim_average_dyn(setup_cte_sim):
'''Test average dynamics.'''
setup_cte_sim['lattice']['S_conc'] = 0
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_avg_dynamics()
assert solution
def test_sim_power_dep_save_txt(setup_cte_sim, mocker):
'''Test that the power dep solution is saved as text correctly'''
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
power_dens_list = np.logspace(1, 2, 3)
solution = sim.simulate_power_dependence(power_dens_list, average=True)
with temp_config_filename('') as filename:
solution.save_txt(filename)
def test_sim_dyn_diff(setup_cte_sim):
'''Test that the two dynamics are different'''
setup_cte_sim['lattice']['S_conc'] = 0
setup_cte_sim['lattice']['A_conc'] = 0.2
with temp_bin_filename() as temp_filename:
sim1 = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution1 = sim1.simulate_dynamics()
solution1.total_error
setup_cte_sim['ions'] = {}
setup_cte_sim['lattice']['S_conc'] = 0.2
setup_cte_sim['lattice']['A_conc'] = 0
with temp_bin_filename() as temp_filename:
sim2 = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution2 = sim2.simulate_dynamics()
solution2.total_error
assert sim1 != sim2
assert solution1 != solution2
def test_sim_dyn_wrong_state_plot(setup_cte_sim):
'''Test that you can't plot a wrong state.'''
setup_cte_sim['lattice']['S_conc'] = 0
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_dynamics()
with pytest.raises(ValueError):
solution.plot(state=10)
plotter.plt.close('all')
def test_sim_conc_dep_save_txt(setup_cte_sim, mocker):
'''Test that the conc dep solution is saved as text correctly'''
with temp_bin_filename() as temp_filename:
conc_list = [(0, 0.3), (0.1, 0.3), (0.1, 0)]
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_concentration_dependence(conc_list,
dynamics=False,
average=True)
with temp_config_filename('') as filename:
solution.save_txt(filename)
def test_sim_dyn_errors(setup_cte_sim):
'''Test that the dynamics work'''
setup_cte_sim['lattice']['S_conc'] = 0
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_dynamics()
solution.errors
assert isinstance(solution.errors, np.ndarray)
solution.log_errors()
def test_sim_power_dep(setup_cte_sim, mocker, average, excitation_name):
'''Test that the power dependence works'''
for exc_name, exc_list in setup_cte_sim.excitations.items():
for exc in exc_list:
if exc_name is excitation_name:
exc.active = True
else:
exc.active = False
with temp_bin_filename() as temp_filename:
mocked = mocker.patch('simetuc.odesolver._solve_ode')
# the num_states changes when the temp lattice is created,
# allocate 2x so that we're safe. Also make the num_points 1000.
mocked.return_value = np.random.random(
(1000, 2 * setup_cte_sim.states['energy_states']))
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
assert sim.cte == setup_cte_sim
power_dens_list = np.logspace(1, 3, 3 - 1 + 1)
solution = sim.simulate_power_dependence(power_dens_list,
average=average)
assert (mocked.call_count
== 2 * len(power_dens_list)) or (mocked.call_count
== len(power_dens_list))
assert solution
solution.plot()
with temp_config_filename('') as filename:
solution.save_txt(filename)
with temp_config_filename('') as filename:
solution.save(filename)
solution_hdf5 = simulations.PowerDependenceSolution.load(filename)
assert solution_hdf5
for sol, sol_hdf5 in zip(solution.solution_list,
solution_hdf5.solution_list):
assert sol.y_sol.shape == sol_hdf5.y_sol.shape
assert np.allclose(sol.t_sol, sol_hdf5.t_sol)
assert np.allclose(sol.y_sol, sol_hdf5.y_sol)
assert sol.cte == sol_hdf5.cte
print(type(sol.index_S_i), type(sol_hdf5.index_S_i))
print(sol.index_S_i, sol_hdf5.index_S_i)
assert sol.index_S_i == sol_hdf5.index_S_i
assert sol.index_A_j == sol_hdf5.index_A_j
assert sol == sol_hdf5
assert solution_hdf5 == solution
solution_hdf5.plot()
plotter.plt.close('all')
def test_optim_save_txt(setup_cte, mocker):
'''Test that the optim solution is saved as text correctly'''
init_param = np.array([proc.value for proc in setup_cte['optimization']['processes']])
def mocked_optim_fun(function, params, sim):
return 2 + (np.array([val for val in params.valuesdict().values()]) - 1.1*init_param)**2
mocker.patch('simetuc.optimize.optim_fun', new=mocked_optim_fun)
with temp_bin_filename() as temp_filename:
solution = optimize.optimize_dynamics(setup_cte, full_path=temp_filename)
with temp_config_filename('') as filename:
solution.save_txt(filename)
def test_sites(setup_cte, sites):
'''Test a lattice with different unit cell parameters
'''
cte = setup_cte
cte['lattice']['sites_pos'] = sites[0]
cte['lattice']['sites_occ'] = sites[1]
with pytest.raises(lattice.LatticeError):
with temp_bin_filename() as temp_filename:
(dist_array, ion_type, doped_lattice, initial_population,
lattice_info, index_S_i, index_A_j, index_S_k, dist_S_k,
index_S_l, dist_S_l, index_A_k, dist_A_k, index_A_l,
dist_A_l) = lattice.generate(cte, full_path=temp_filename)
def test_unit_cell(setup_cte, cell_params):
'''Test a lattice with different unit cell parameters
'''
cte = setup_cte
for key, param in zip(['a', 'b', 'c', 'alpha', 'beta', 'gamma'],
cell_params):
cte.lattice[key] = param
with pytest.raises(lattice.LatticeError):
with temp_bin_filename() as temp_filename:
(dist_array, ion_type, doped_lattice, initial_population,
lattice_info, index_S_i, index_A_j, index_S_k, dist_S_k,
index_S_l, dist_S_l, index_A_k, dist_A_k, index_A_l,
dist_A_l) = lattice.generate(cte, full_path=temp_filename)
def test_sim_dyn(setup_cte_sim):
'''Test that the dynamics work'''
setup_cte_sim['lattice']['S_conc'] = 0
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
assert sim.cte == setup_cte_sim
solution = sim.simulate_dynamics()
assert solution
solution.plot()
solution.plot(state=7)
solution.plot(state=1)
plotter.plt.close('all')
def test_optim_wrong_method(setup_cte, mocker):
'''Test that the optimization works without the optimization params being present in cte'''
# mock the simulation by returning an error that goes to 0
init_param = np.array([proc.value for proc in setup_cte['optimization']['processes']])
def mocked_optim_fun(function, params, sim):
return 2 + (np.array([val for val in params.valuesdict().values()]) - 1.1*init_param)**2
mocker.patch('simetuc.optimize.optim_fun', new=mocked_optim_fun)
setup_cte['optimization']['method'] = 'wrong_method'
with pytest.raises(ValueError) as excinfo:
with temp_bin_filename() as temp_filename:
optimize.optimize_dynamics(setup_cte, full_path=temp_filename)
assert excinfo.match(r"Wrong optimization method")
assert excinfo.type == ValueError
def test_sim_conc_dep_empty_conc(setup_cte_sim):
'''Conc list is empty'''
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
conc_list = []
solution = sim.simulate_concentration_dependence(conc_list)
with pytest.warns(plotter.PlotWarning) as warnings:
solution.plot()
# assert len(warnings) == 1 # one warning
warning = warnings.pop(plotter.PlotWarning)
assert issubclass(warning.category, plotter.PlotWarning)
assert 'Nothing to plot! The concentration_dependence list is emtpy!' in str(
warning.message)
plotter.plt.close('all')
def test_sim_power_dep_correct_power_dens(setup_cte_sim, mocker):
'''Check that the solutions have the right power_dens'''
setup_cte_sim['no_plot'] = True
with temp_bin_filename() as temp_filename:
mocked = mocker.patch('simetuc.odesolver._solve_ode')
# the num_states changes when the temp lattice is created,
# allocate 2x so that we're safe. Also make the num_points 1000.
mocked.return_value = np.random.random(
(1000, 2 * setup_cte_sim['states']['energy_states']))
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
power_dens_list = np.logspace(1, 3, 3)
solution = sim.simulate_power_dependence(power_dens_list)
assert mocked.call_count == 2 * len(power_dens_list)
for num, pow_dens in enumerate(power_dens_list):
assert solution[num].power_dens == pow_dens
def test_sim_sample_dynamics(setup_cte_sim, mocker, N_samples):
'''Test that sampling the dynamics works'''
setup_cte_sim['lattice']['S_conc'] = 0
mocked = mocker.patch('simetuc.odesolver._solve_ode')
# the num_states changes when the temp lattice is created,
# allocate 2x so that we're safe. Also make the num_points 1000.
mocked.return_value = np.random.random(
(1000, 2 * setup_cte_sim.states['energy_states']))
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
assert sim.cte == setup_cte_sim
solution = sim.sample_simulation(sim.simulate_dynamics,
N_samples=N_samples)
assert solution
assert mocked.call_count == 2 * N_samples
def test_sim_no_plot(setup_cte_sim):
'''Test that no plot works'''
setup_cte_sim['no_plot'] = True
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_dynamics()
with pytest.warns(plotter.PlotWarning) as warnings:
solution.plot()
# assert len(warnings) == 1 # one warning
warning = warnings.pop(plotter.PlotWarning)
assert issubclass(warning.category, plotter.PlotWarning)
assert 'A plot was requested, but no_plot setting is set' in str(
warning.message)
plotter.plt.close('all')
def test_sim_conc_dep_only_S(setup_cte_sim, mocker):
'''Conc list has only S changing'''
with temp_bin_filename() as temp_filename:
mocked = mocker.patch('simetuc.odesolver._solve_ode')
# the num_states changes when the temp lattice is created,
# allocate 2x so that we're safe. Also make the num_points 1000.
mocked.return_value = np.random.random(
(1000, 2 * setup_cte_sim['states']['energy_states']))
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
conc_list = [(0.01, 0.3), (0.1, 0.3), (0.3, 0.3)]
solution = sim.simulate_concentration_dependence(conc_list,
dynamics=False)
assert mocked.call_count == 2 * len(conc_list)
assert solution
solution.plot()
plotter.plt.close('all')
def test_sim_conc_dep_list(setup_cte_sim, mocker):
'''Test that the concentration dependence works'''
with temp_bin_filename() as temp_filename:
mocked = mocker.patch('simetuc.odesolver._solve_ode')
# the num_states changes when the temp lattice is created,
# allocate 2x so that we're safe. Also make the num_points 1000.
mocked.return_value = np.random.random(
(1000, 2 * setup_cte_sim['states']['energy_states']))
conc_list = [(0, 0.3), (0.1, 0.3), (0.1, 0)]
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
solution = sim.simulate_concentration_dependence(conc_list,
dynamics=True)
# dynamics call solve_ode twice (pulse and relaxation)
assert mocked.call_count == 2 * len(conc_list)
for num, conc in enumerate(conc_list):
assert solution[num].concentration == conc
def test_optim_no_dict_params(setup_cte, mocker):
'''Test that the optimization works with an empty optimization dict'''
# mock the simulation by returning an error that goes to 0
init_param = np.array([proc.value for proc in setup_cte.energy_transfer.values() if proc.value != 0])
def mocked_optim_fun(function, params, sim):
return 2 + (np.array([val for val in params.valuesdict().values()]) - 1.1*init_param)**2
mocker.patch('simetuc.optimize.optim_fun', new=mocked_optim_fun)
setup_cte['optimization'] = {}
setup_cte['optimization']['processes'] = [proc for proc in setup_cte.energy_transfer.values() if proc.value != 0]
setup_cte['optimization']['options'] = {}
with temp_bin_filename() as temp_filename:
optim_solution = optimize.optimize_dynamics(setup_cte, full_path=temp_filename)
best_x = optim_solution.best_params
min_f = optim_solution.min_f
res = optim_solution.result
assert len(best_x) == len(init_param)
assert min_f == np.sqrt((res.residual**2).sum())
def test_cte_wrong(setup_cte, params):
'''Test a lattice with different unit cell parameters
'''
cte = setup_cte
cte['lattice']['S_conc'] = params[0]
cte['lattice']['A_conc'] = params[1]
cte['lattice']['N_uc'] = params[2]
cte['states']['sensitizer_states'] = params[3]
cte['states']['activator_states'] = params[4]
if params[5] is not None:
cte['lattice']['radius'] = params[5]
del cte['lattice']['N_uc']
with pytest.raises(lattice.LatticeError):
with temp_bin_filename() as temp_filename:
(dist_array, ion_type, doped_lattice, initial_population,
lattice_info, index_S_i, index_A_j, index_S_k, dist_S_k,
index_S_l, dist_S_l, index_A_k, dist_A_k, index_A_l,
dist_A_l) = lattice.generate(cte, full_path=temp_filename)
def test_sim_steady1(setup_cte_sim):
'''Test that the steady state solution is saved a loaded correctly'''
setup_cte_sim['excitations']['Vis_473'][0].t_pulse = 1e-08
with temp_bin_filename() as temp_filename:
sim = simulations.Simulations(setup_cte_sim, full_path=temp_filename)
assert sim.cte == setup_cte_sim
solution = sim.simulate_steady_state()
assert solution
solution.log_populations()
solution.plot()
solution.log_populations() # redo
with temp_config_filename('') as filename:
solution.save(filename)
sol_hdf5 = simulations.SteadyStateSolution.load(filename)
assert sol_hdf5
assert sol_hdf5 == solution
sol_hdf5.plot()
plotter.plt.close('all')
def test_optim(setup_cte, mocker, method, function, average, processes, excitations, N_samples):
'''Test that the optimization works'''
# mock the simulation by returning an error that goes to 0
init_param = np.array([proc.value for proc in processes])
def mocked_optim_fun(function, params, sim):
return 2 + (np.array([val for val in params.valuesdict().values()]) - 1.1*init_param)**2
mocker.patch('simetuc.optimize.optim_fun', new=mocked_optim_fun)
setup_cte['optimization']['method'] = method
setup_cte['optimization']['processes'] = processes
setup_cte['optimization']['excitations'] = excitations
fun = getattr(optimize, function)
with warnings.catch_warnings(), temp_bin_filename() as temp_filename:
warnings.filterwarnings("ignore", message="divide by zero encountered in double_scalars")
optim_solution = fun(setup_cte, average=average, full_path=temp_filename, N_samples=N_samples)
best_x = optim_solution.best_params
min_f = optim_solution.min_f
res = optim_solution.result
assert len(best_x) == len(processes)
if method in 'brute':
assert min_f == np.sqrt(res.candidates[0].score)
else:
assert min_f == np.sqrt((res.residual**2).sum())
def test_single_atom(setup_cte, concs):
'''Generate lattices with a single S or A'''
cte = setup_cte
cte['lattice']['N_uc'] = 1
cte['states']['sensitizer_states'] = 2
cte['states']['activator_states'] = 7
# single A atom
success = False
cte['lattice']['S_conc'] = concs[0]
cte['lattice']['A_conc'] = concs[1]
while not success:
try:
with temp_bin_filename() as temp_filename:
(dist_array, ion_type, doped_lattice, initial_population,
lattice_info, index_S_i, index_A_j, index_S_k, dist_S_k,
index_S_l, dist_S_l, index_A_k, dist_A_k, index_A_l,
dist_A_l) = lattice.generate(cte, full_path=temp_filename)
except lattice.LatticeError: # no ions were generated, repeat
pass
else:
if len(ion_type) == 1: # only one ion was generated
success = True
