import pytest import numpy as np import openpnm as op import numpy.testing as nt class TransportTest: def setup_class(self): self.net = op.network.Cubic(shape=[9, 9, 9]) self.net.add_model_collection( op.models.collections.geometry.spheres_and_cylinders) self.net.regenerate_models() self.phase = op.phase.Air(network=self.net) self.phase.add_model_collection( op.models.collections.physics.basic) self.phase.regenerate_models() self.phase['pore.mole_fraction'] = 0 self.phase['throat.diffusive_conductance'] = 1.0 def test_undefined_elements(self): net = op.network.Cubic(shape=[3, 3, 3]) phase = op.phase.Phase(network=net) phase["throat.conductance"] = 1.0 alg = op.algorithms.Transport(network=net, phase=phase) alg.settings._update({"quantity": "pore.concentration", "conductance": "throat.conductance"}) def test_remove_boundary_conditions(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.set_value_BC(pores=self.net.pores('top'), values=1) alg.set_value_BC(pores=self.net.pores('bottom'), values=0) assert np.sum(np.isfinite(alg['pore.bc.value'])) > 0 alg.set_value_BC(pores=self.net.pores('top'), mode='remove') assert np.sum(np.isfinite(alg['pore.bc.value'])) > 0 alg.set_value_BC(pores=self.net.pores('bottom'), mode='remove') assert np.sum(np.isfinite(alg['pore.bc.value'])) == 0 def test_generic_transport(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_value_BC(pores=self.net.pores('top'), values=1) alg.set_value_BC(pores=self.net.pores('bottom'), values=0) alg.run() from openpnm.algorithms._solution import SteadyStateSolution quantity = alg.settings['quantity'] # Ensure solution object is attached to the algorithm assert isinstance(alg.soln[quantity], SteadyStateSolution) def test_ill_defined_topology(self): net = op.network.Cubic(shape=[5, 1, 1]) op.topotools.trim(net, pores=[2]) phase = op.phase.Phase(network=net) phase["throat.diffusive_conductance"] = 1.0 alg = op.algorithms.Transport(network=net, phase=phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_value_BC(pores=net.pores('left'), values=1) with pytest.raises(Exception): alg.run() def test_linear_system_with_nans_or_infs(self): net = op.network.Cubic(shape=[5, 1, 1]) phase = op.phase.Phase(network=net) phase["throat.diffusive_conductance"] = 1.0 alg = op.algorithms.Transport(network=net, phase=phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_value_BC(pores=net.pores('left'), values=1) # A contains nan with pytest.raises(Exception): phase["throat.diffusive_conductance"][1] = np.inf alg.run() phase["throat.diffusive_conductance"] = 1.0 # A contains inf with pytest.raises(Exception): phase["throat.diffusive_conductance"][1] = np.inf alg.run() phase["throat.diffusive_conductance"] = 1.0 # b contains nan with pytest.raises(Exception): phase["throat.diffusive_conductance"][1] = np.inf alg.run() phase["throat.diffusive_conductance"] = 1.0 # b contains inf with pytest.raises(Exception): phase["throat.diffusive_conductance"][1] = np.inf alg.run() def test_ill_defined_settings(self): net = op.network.Cubic(shape=[5, 1, 1]) phase = op.phase.Phase(network=net) phase["throat.diffusive_conductance"] = 1.0 alg = op.algorithms.Transport(network=net, phase=phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_value_BC(pores=net.pores('left'), values=1) # conductance is not defined with pytest.raises(Exception): alg.settings['conductance'] = None alg.run() alg.settings['conductance'] = 'throat.diffusive_conductance' # quantity is not defined with pytest.raises(Exception): alg.settings['quantity'] = None alg.run() alg.settings['quantity'] = 'pore.mole_fraction' # phase is not defined with pytest.raises(Exception): alg.settings['phase'] = None alg.run() def test_two_value_conditions(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_value_BC(pores=self.net.pores('top'), values=1) alg.set_value_BC(pores=self.net.pores('bottom'), values=0) alg.run() x = [0.0, 0.125, 0.25, 0.375, 0.5, 0.625, 0.75, 0.875, 1.0] y = np.unique(np.around(alg['pore.mole_fraction'], decimals=3)) assert np.all(x == y) def test_one_value_one_rate(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_rate_BC(pores=self.net.pores('bottom'), rates=1) alg.set_value_BC(pores=self.net.pores('top'), values=0) alg.run() x = [0., 1., 2., 3., 4., 5., 6., 7., 8.] y = np.unique(np.around(alg['pore.mole_fraction'], decimals=3)) assert np.all(x == y) def test_set_value_bc_where_rate_is_already_set_mode_merge(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_rate_BC(pores=[0, 1], rates=1, mode='add') with pytest.raises(Exception): alg.set_value_BC(pores=[1, 2], values=0, mode='add') assert np.isfinite(alg['pore.bc.rate']).sum() == 2 assert np.isfinite(alg['pore.bc.value']).sum() == 0 alg.set_rate_BC(pores=[0, 1], rates=1, mode='overwrite') alg.set_value_BC(pores=[1, 2], values=0, mode='overwrite') assert np.isfinite(alg['pore.bc.rate']).sum() == 1 assert np.isfinite(alg['pore.bc.value']).sum() == 2 def test_cache(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_rate_BC(pores=self.net.pores('bottom'), rates=1) alg.set_value_BC(pores=self.net.pores('top'), values=0) alg.settings["cache"] = True alg.run() x_before = alg["pore.mole_fraction"].mean() self.phase["throat.diffusive_conductance"][1] = 50.0 alg.run() x_after = alg["pore.mole_fraction"].mean() # When cache is True, A is not recomputed, hence x == y assert x_before == x_after alg.settings["cache"] = False alg.run() x_after = alg["pore.mole_fraction"].mean() # When cache is False, A must be recomputed, hence x!= y assert x_before != x_after # Revert back changes to objects self.setup_class() def test_rate_single_pore(self): alg = op.algorithms.ReactiveTransport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' pores = self.net.pores("left") alg.set_rate_BC(pores=pores, rates=1.235*np.ones(pores.size)) alg.set_value_BC(pores=self.net.pores("right"), values=0.0) alg.run() rate = alg.rate(pores=self.net.pores("right"))[0] assert np.isclose(rate, -1.235*self.net.pores("right").size) # Net rate must always be zero at steady state conditions assert np.isclose(alg.rate(pores=self.net.Ps), 0.0) def test_rate_multiple_pores(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_rate_BC(pores=[0, 1, 2, 3], rates=1.235) alg.set_rate_BC(pores=[5, 6, 19, 35, 0], rates=3.455, mode='overwrite') # Pore 0 is assigned two rate BCs, only the most recent will be kept alg.set_value_BC(pores=[50, 51, 52, 53], values=0.0) alg.run() rate = alg.rate(pores=[50, 51, 52, 53])[0] # 3 and 5 are number of pores in each rate BC assert np.isclose(rate, -(1.235*3 + 3.455*5)) # Net rate must always be zero at steady state conditions assert np.isclose(alg.rate(pores=self.net.Ps), 0.0) def test_rate_multiple_values(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_rate_BC(pores=[0, 1, 2, 3], rates=[0, 3.5, 0.4, -12]) alg.set_value_BC(pores=[50, 51, 52, 53], values=0.0) alg.run() rate_individual = alg.rate(pores=[0, 1, 2, 3], mode='single') rate_net = alg.rate(pores=[0, 1, 2, 3], mode='group')[0] nt.assert_allclose(rate_individual, [0, 3.5, 0.4, -12], atol=1e-10) nt.assert_allclose(rate_net, sum([0, 3.5, 0.4, -12])) # def test_rate_Nt_by_2_conductance(self): # net = op.network.Cubic(shape=[1, 6, 1]) # net.add_model_collection( # op.models.collections.geometry.spheres_and_cylinders) # net.regenerate_models() # air = op.phase.Air(network=net) # water = op.phase.Water(network=net) # m = op.contrib.MultiPhase(network=net, phases=[air, water]) # m.set_occupancy(phase=air, pores=[0, 1, 2]) # m.set_occupancy(phase=water, pores=[3, 4, 5]) # const = op.models.misc.constant # K_water_air = 0.5 # m.set_binary_partition_coef(phases=[water, air], model=const, value=K_water_air) # m._set_automatic_throat_occupancy() # alg = op.algorithms.Transport(network=net, phase=m) # alg.settings['conductance'] = 'throat.diffusive_conductance' # alg.settings['quantity'] = 'pore.mole_fraction' # alg.set_rate_BC(pores=0, values=1.235) # alg.set_value_BC(pores=5, values=0.0) # alg.run() # rate = alg.rate(pores=5)[0] # assert np.isclose(rate, -1.235) # # Rate at air-water interface throat (#2) must match imposed rate # rate = alg.rate(throats=2)[0] # assert np.isclose(rate, 1.235) # # Rate at interface pores (#2 @ air-side, #3 @ water-side) must be 0 # rate_air_side = alg.rate(pores=2)[0] # rate_water_side = alg.rate(pores=3)[0] # assert np.isclose(rate_air_side, 0.0) # assert np.isclose(rate_water_side, 0.0) # # Net rate must always be zero at steady state conditions # assert np.isclose(alg.rate(pores=net.Ps), 0.0) # def test_reset_settings_and_data(self): # alg = op.algorithms.Transport(network=self.net, # phase=self.phase) # alg.settings['conductance'] = 'throat.diffusive_conductance' # alg.settings['quantity'] = 'pore.mole_fraction' # alg.set_rate_BC(pores=self.net.pores('bottom'), values=1) # alg.set_value_BC(pores=self.net.pores('top'), values=0) # alg.run() # assert ~np.all(np.isnan(alg['pore.bc.value'])) # assert ~np.all(np.isnan(alg['pore.bc.rate'])) # assert 'pore.mole_fraction' in alg.keys() # alg.reset(bcs=True, results=False) # assert np.all(np.isnan(alg['pore.bc.value'])) # assert np.all(np.isnan(alg['pore.bc.rate'])) # assert 'pore.mole_fraction' in alg.keys() # alg.reset(bcs=True, results=True) # assert 'pore.mole_fraction' not in alg.keys() # alg.set_rate_BC(pores=self.net.pores('bottom'), values=1) # alg.set_value_BC(pores=self.net.pores('top'), values=0) # alg.run() # def test_reset_actual_results(self): # alg = op.algorithms.Transport(network=self.net, # phase=self.phase) # alg.settings['conductance'] = 'throat.diffusive_conductance_temp' # self.phase['throat.diffusive_conductance_temp'] = 1.0 # alg.settings['quantity'] = 'pore.concentration' # alg.set_value_BC(pores=self.net.pores('bottom'), values=1) # alg.set_value_BC(pores=self.net.pores('top'), values=0) # alg.run() # m1 = alg.rate(pores=self.net.pores('top')) # m2 = -alg.rate(pores=self.net.pores('bottom')) # # This should pass because the alg has only run once # np.testing.assert_allclose(m1, m2) # # Now adjust conductance values and re-run # self.phase['throat.diffusive_conductance_temp'][[0, 1, 2]] *= 0.1 # alg.run() # m1 = alg.rate(pores=self.net.pores('top')) # m2 = -alg.rate(pores=self.net.pores('bottom')) # # The mass won't balance, so the same test will fail # with pytest.raises(AssertionError): # np.testing.assert_allclose(m1, m2) # # Now use reset method # alg.reset() # alg.run() # m1 = alg.rate(pores=self.net.pores('top')) # m2 = -alg.rate(pores=self.net.pores('bottom')) # # Now this will pass again # np.testing.assert_allclose(m1, m2) # def test_validate_data_health(self): # alg = op.algorithms.Transport(network=self.net, # phase=self.phase) # alg.settings['conductance'] = 'throat.diffusive_conductance' # alg.settings['quantity'] = 'pore.concentration' # alg.settings['cache'] = False # alg.set_value_BC(pores=self.net.pores('top'), values=1) # alg.set_value_BC(pores=self.net.pores('bottom'), values=0) # # Check if the method can catch NaNs in data # self.phase['throat.diffusive_conductance'][0] = np.nan # with pytest.raises(Exception): # alg.run() # mod = op.models.misc.from_neighbor_pores # self.phase["pore.seed"] = np.nan # self.phys.add_model(propname="throat.diffusive_conductance", model=mod, # prop="pore.seed", ignore_nans=False) # with pytest.raises(Exception): # alg.run() # self.phase["pore.seed"] = 1 # self.phase.regenerate_models(propnames="throat.diffusive_conductance") # # Check if the method can catch unhealthy topology # Ts = self.net.find_neighbor_throats(pores=0) # op.topotools.trim(self.net, throats=Ts) # with pytest.raises(Exception): # alg.run() # # Reset network back to original # self.setup_class() # def test_total_rate(self): # alg = op.algorithms.GenericTransport(network=self.net, # phase=self.phase) # h = op.utils.check_network_health(self.net) # op.topotools.trim(self.net, pores=h['disconnected_pores']) # alg.settings['conductance'] = 'throat.diffusive_conductance' # alg.settings['quantity'] = 'pore.mole_fraction' # alg.set_rate_BC(pores=[0, 1, 2, 3], total_rate=1) # alg.set_value_BC(pores=[50, 51, 52, 53], values=0.0) # alg.run() # rate_individual = alg.rate(pores=[0, 1, 2, 3], mode='single') # nt.assert_allclose(rate_individual, [0.25, 0.25, 0.25, 0.25], # atol=1e-10) # # test exceptions that come from adding total_rate feature # with pytest.raises(Exception): # alg.set_rate_BC(pores=[0, 1, 2, 3], # total_rate=[0.25, 0.25, 0.25, 0.25]) # with pytest.raises(Exception): # alg.set_rate_BC(pores=[0, 1, 2, 3], rates=1, total_rate=1) # def test_network_continuity(self): # net = op.network.Cubic([5, 1, 1]) # op.topotools.trim(network=net, pores=[2]) # phase = op.phase.Phase(network=net) # phase['throat.diffusive_conductance'] = 1.0 # alg = op.algorithms.FickianDiffusion(network=net, phase=phase) # alg.set_value_BC(pores=0, values=1) # with pytest.raises(Exception): # alg.run() # alg.set_value_BC(pores=3, values=0) # alg.run() def test_x0_is_nan(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) alg.settings['conductance'] = 'throat.diffusive_conductance' alg.settings['quantity'] = 'pore.mole_fraction' alg.set_value_BC(pores=self.net.pores('top'), values=1) alg.set_value_BC(pores=self.net.pores('bottom'), values=0) x0 = np.zeros(alg.Np) x0[5] = np.nan with pytest.raises(Exception): alg.run(x0=x0) def test_get_source_list(self): alg = op.algorithms.Transport(network=self.net, phase=self.phase) assert alg['pore.source'] == {} with pytest.raises(KeyError): alg['pore.source_blah'] == {} def teardown_class(self): ws = op.Workspace() ws.clear() if __name__ == '__main__': t = TransportTest() t.setup_class() self = t for item in t.__dir__(): if item.startswith('test'): print(f'Running test: {item}') t.__getattribute__(item)()