File size: 18,286 Bytes
f421c2e | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 | 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)()
|