Merge pull request #578 from PMEAL/fix_issue_566

Fix issue #566

OpenPNM/Physics/models/hydraulic_conductance.py

@@ -9,10 +9,13 @@
 import OpenPNM.Utilities.misc as misc
 
 
-def hagen_poiseuille(physics, phase, network, pore_diameter='pore.diameter',
-                     pore_viscosity='pore.viscosity', throat_length='throat.length',
-                     throat_diameter='throat.diameter', calc_pore_len=True,
+def hagen_poiseuille(physics, phase, network,
+                     pore_diameter='pore.diameter',
+                     pore_viscosity='pore.viscosity',
+                     throat_length='throat.length',
+                     throat_diameter='throat.diameter',
                      shape_factor='throat.shape_factor',
+                     calc_pore_len=False,
                      **kwargs):
     r"""
     Calculates the hydraulic conductivity of throat assuming cylindrical
@@ -26,11 +29,8 @@ def hagen_poiseuille(physics, phase, network, pore_diameter='pore.diameter',
 
     Notes
     -----
-    (1) This function requires that all the necessary phase properties already
-    be calculated.
-
-    (2) This function calculates the specified property for the *entire*
-    network then extracts the values for the appropriate throats at the end.
+    This function calculates the specified property for the *entire* network
+    then extracts the values for the appropriate throats at the end.
 
     """
     # Get Nt-by-2 list of pores connected to each throat

OpenPNM/Utilities/misc.py

@@ -271,13 +271,13 @@ def conduit_lengths(network, throats=None, mode='pore'):
         # Find the pore-to-pore distance, minus the throat length
         lengths = _sp.sqrt(_sp.sum(_sp.square(pcoords[Ps[:, 0]] -
                                    pcoords[Ps[:, 1]]), 1)) - network['throat.length']
-        lengths[lengths <= 0.0] = 2e-9
+        lengths[lengths < 0.0] = 2e-9
         # Calculate the fraction of that distance from the first pore
         try:
             fractions = pdia[Ps[:, 0]]/(pdia[Ps[:, 0]] + pdia[Ps[:, 1]])
             # Don't allow zero lengths
-            fractions[fractions == 0.0] = 0.5
-            fractions[fractions == 1.0] = 0.5
+#            fractions[fractions == 0.0] = 0.5
+#            fractions[fractions == 1.0] = 0.5
         except:
             fractions = 0.5
         plen1 = lengths*fractions

run_script.py

@@ -5,16 +5,20 @@
 #==============================================================================
 '''Build Topological Network'''
 #==============================================================================
-pn = op.Network.Cubic(shape=[5,6,7],spacing=0.0001,name='net')
+pn = op.Network.Cubic(shape=[5,5,5],spacing=1,name='net')
 pn.add_boundaries()
 
 #==============================================================================
 '''Build Geometry'''
 #==============================================================================
 Ps = pn.pores('boundary',mode='not')
 Ts = pn.find_neighbor_throats(pores=Ps,mode='intersection',flatten=True)
-geom = op.Geometry.Toray090(network=pn,pores=Ps,throats=Ts)
-geom.models.add(propname='throat.length',model=gm.throat_length.straight)
+geom = op.Geometry.GenericGeometry(network=pn,pores=Ps,throats=Ts)
+geom['throat.length'] = 0
+geom['throat.diameter'] = 1
+geom['pore.diameter'] = 1
+geom['pore.area'] = 1
+geom['throat.area'] = 1
 Ps = pn.pores('boundary')
 Ts = pn.find_neighbor_throats(pores=Ps,mode='not_intersection')
 boun = op.Geometry.Boundary(network=pn,pores=Ps,throats=Ts)
@@ -67,27 +71,18 @@
 BC2_pores = pn.pores('left_boundary')
 alg.set_boundary_conditions(bctype='Dirichlet', bcvalue=0.4, pores=BC2_pores)
 #Add new model to air's physics that accounts for water occupancy
-phys_air.models.add(model=op.Physics.models.multiphase.conduit_conductance,
-                    propname='throat.conduit_diffusive_conductance',
-                    throat_conductance='throat.diffusive_conductance',
-                    throat_occupancy='throat.occupancy',
-                    pore_occupancy='pore.occupancy',
-                    mode='strict',
-                    factor=0)
+#phys_air.models.add(model=op.Physics.models.multiphase.conduit_conductance,
+#                    propname='throat.conduit_diffusive_conductance',
+#                    throat_conductance='throat.diffusive_conductance',
+#                    throat_occupancy='throat.occupancy',
+#                    pore_occupancy='pore.occupancy',
+#                    mode='strict',
+#                    factor=0)
 #Use desired diffusive_conductance in the diffusion calculation (conductance for the dry network or water-filled network)
 alg.run(conductance='throat.diffusive_conductance')
 alg.return_results()
 Deff = alg.calc_eff_diffusivity()
-
-try:
-    # this creates a time step x num_pores, which is what the animated object needs
-    inv_seq = water['pore.IP_inv_seq'].squeeze()
-    history = []
-    for i in sorted(set(inv_seq)):
-      history.append( (inv_seq != 0) & (inv_seq < i) )
-
-except Exception as e:
-    pass
+print(Deff/air['pore.diffusivity'][0])
 
 #------------------------------------------------------------------------------
 '''Export to VTK'''

test/unit/Physics/GenericPhysicsTest.py

@@ -1,5 +1,6 @@
 import OpenPNM
 import scipy as sp
+import pytest
 
 
 class GenericPhysicsTest:
@@ -23,35 +24,23 @@ def setup_class(self):
                                                     geometry=self.geo1)
 
     def test_specify_pores_and_geometry(self):
-        flag = False
-        try:
+        with pytest.raises(Exception):
             OpenPNM.Physics.GenericPhysics(network=self.net,
                                            phase=self.phase1,
                                            geometry=self.geo1,
                                            pores=[0])
-        except:
-            flag = True
-        assert flag
 
     def test_specify_overlapping_pores(self):
-        flag = False
-        try:
+        with pytest.raises(Exception):
             OpenPNM.Physics.GenericPhysics(network=self.net,
                                            phase=self.phase1,
                                            pores=[0])
-        except:
-            flag = True
-        assert flag
 
     def test_specify_overlapping_geometry(self):
-        flag = False
-        try:
+        with pytest.raises(Exception):
             OpenPNM.Physics.GenericPhysics(network=self.net,
                                            phase=self.phase1,
                                            geometry=self.geo1)
-        except:
-            flag = True
-        assert flag
 
     def test_get_item_self_name(self):
         a = self.phys1.get('pore.'+self.phys1.name)
@@ -119,8 +108,15 @@ def test_reassign_phase_regenerate_models(self):
                                               geometry=geo1)
         phys.models.add(propname='throat.hydraulic_conductance',
                         model=physmods.hydraulic_conductance.hagen_poiseuille)
-        assert sp.allclose(phys['throat.hydraulic_conductance'], 0.02454369)
+        # Get value of hydraulic_conductance in current phys
+        a = phys['throat.hydraulic_conductance'][0]
+        # Make sure they're all the same
+        assert sp.allclose(phys['throat.hydraulic_conductance'], a)
+        # Assign phys to a different phase with 10x higher viscoity
         phys.parent_phase = phase2
-        assert sp.allclose(phys['throat.hydraulic_conductance'], 0.02454369)
+        # Verify that hydraulic_conductance has NOT yet changed
+        assert sp.allclose(phys['throat.hydraulic_conductance'], a)
+        # Re-run models
         phys.models.regenerate()
-        assert sp.allclose(phys['throat.hydraulic_conductance'], 0.00245437)
+        # Confirm hydraulic_conductance is 10x lower
+        assert sp.allclose(phys['throat.hydraulic_conductance'], a/10)

test/unit/Physics/models/DiffusiveConductanceTest.py

@@ -1,3 +1,33 @@
+import OpenPNM
+import pytest
+import scipy as sp
+
+
 class DiffusiveConductanceTest:
+    def setup_class(self):
+        self.net = OpenPNM.Network.Cubic(shape=[5, 5, 5], spacing=1.0)
+        self.geo = OpenPNM.Geometry.GenericGeometry(network=self.net,
+                                                    pores=self.net.Ps,
+                                                    throats=self.net.Ts)
+        self.geo['pore.diameter'] = 1.0
+        self.geo['pore.area'] = 1.0
+        self.geo['throat.diameter'] = 1.0
+        self.geo['throat.length'] = 1e-9
+        self.geo['throat.area'] = 1
+        self.air = OpenPNM.Phases.Air(network=self.net)
+        self.phys = OpenPNM.Physics.GenericPhysics(network=self.net,
+                                                   phase=self.air,
+                                                   geometry=self.geo)
+
     def test_bulk_diffusion(self):
-        pass
+        mod = OpenPNM.Physics.models.diffusive_conductance.bulk_diffusion
+        self.phys.models.add(propname='throat.conductance1',
+                             model=mod)
+        assert sp.allclose(a=self.phys['throat.conductance1'][0],
+                           b=0.00084552)
+
+        self.phys.models.add(propname='throat.conductance2',
+                             model=mod,
+                             calc_pore_len=True)
+        assert sp.allclose(a=self.phys['throat.conductance2'][0],
+                           b=0.00084552)

test/unit/Physics/models/HydraulicConductance.py

@@ -0,0 +1,31 @@
+import OpenPNM
+import pytest
+import scipy as sp
+
+
+class HydraulicConductanceTest:
+    def setup_class(self):
+        self.net = OpenPNM.Network.Cubic(shape=[5, 5, 5], spacing=1.0)
+        self.geo = OpenPNM.Geometry.GenericGeometry(network=self.net,
+                                                    pores=self.net.Ps,
+                                                    throats=self.net.Ts)
+        self.geo['pore.diameter'] = 1.0
+        self.geo['throat.diameter'] = 1.0
+        self.geo['throat.length'] = 1.0e-9
+        self.air = OpenPNM.Phases.Air(network=self.net)
+        self.phys = OpenPNM.Physics.GenericPhysics(network=self.net,
+                                                   phase=self.air,
+                                                   geometry=self.geo)
+
+    def test_hagen_poiseuille(self):
+        mod = OpenPNM.Physics.models.hydraulic_conductance.hagen_poiseuille
+        self.phys.models.add(propname='throat.conductance1',
+                             model=mod)
+        assert sp.allclose(a=self.phys['throat.conductance1'][0],
+                           b=1330.68207684)
+
+        self.phys.models.add(propname='throat.conductance2',
+                             model=mod,
+                             calc_pore_len=True)
+        assert sp.allclose(a=self.phys['throat.conductance2'][0],
+                           b=1330.68207684)