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Fixing in pore scale models #2889

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merged 4 commits into from
Jan 26, 2024
Merged

Fixing in pore scale models #2889

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9e31311
Fixed bug in pore surface area models
jgostick Jan 26, 2024
c6a4333
updating tests
jgostick Jan 26, 2024
93b5bb5
updating tests
jgostick Jan 26, 2024
51c3715
adding check to prevent negative numbers
jgostick Jan 26, 2024
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16 changes: 12 additions & 4 deletions openpnm/models/geometry/pore_surface_area/_funcs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,9 @@ def sphere(
R = network[pore_diameter] / 2
value = 4 * _np.pi * R**2
Tca = network[throat_cross_sectional_area]
_np.subtract.at(value, network.conns.T.flatten(), _np.repeat(Tca, repeats=2))
_np.subtract.at(value, network.conns[:, 0], Tca)
_np.subtract.at(value, network.conns[:, 1], Tca)
value = _np.clip(value, 1e-12, _np.inf)
return value


Expand Down Expand Up @@ -69,7 +71,9 @@ def circle(
"""
value = _np.pi * network[pore_diameter]
Tca = network[throat_cross_sectional_area]
_np.subtract.at(value, network.conns.T.flatten(), _np.repeat(Tca, repeats=2))
_np.subtract.at(value, network.conns[:, 0], Tca)
_np.subtract.at(value, network.conns[:, 1], Tca)
value = _np.clip(value, 1e-12, _np.inf)
return value


Expand All @@ -95,7 +99,9 @@ def cube(
D = network[pore_diameter]
value = 6.0 * D**2
Tca = network[throat_cross_sectional_area]
_np.subtract.at(value, network.conns.T.flatten(), _np.repeat(Tca, repeats=2))
_np.subtract.at(value, network.conns[:, 0], Tca)
_np.subtract.at(value, network.conns[:, 1], Tca)
value = _np.clip(value, 1e-12, _np.inf)
return value


Expand All @@ -121,5 +127,7 @@ def square(
D = network[pore_diameter]
value = 4.0 * D
Tca = network[throat_cross_sectional_area]
_np.subtract.at(value, network.conns.T.flatten(), _np.repeat(Tca, repeats=2))
_np.subtract.at(value, network.conns[:, 0], Tca)
_np.subtract.at(value, network.conns[:, 1], Tca)
value = _np.clip(value, 1e-12, _np.inf)
return value
18 changes: 9 additions & 9 deletions tests/unit/models/geometry/PoreSurfaceAreaTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ def test_sphere(self):

def test_circle(self):
self.net2D.add_model(propname='pore.surface_area',
model=mods.circle,
regen_mode='normal')
model=mods.circle,
regen_mode='normal')
a = np.array([2.74159265, 2.84159265, 2.94159265])
b = np.unique(self.net2D['pore.surface_area'])
assert_allclose(a, b)
Expand All @@ -39,8 +39,8 @@ def test_cube(self):

def test_square(self):
self.net2D.add_model(propname='pore.surface_area',
model=mods.square,
regen_mode='normal')
model=mods.square,
regen_mode='normal')
a = np.array([3.6, 3.7, 3.8])
b = np.unique(self.net2D['pore.surface_area'])
assert_allclose(a, b)
Expand All @@ -54,16 +54,16 @@ def test_circle_multi_geom(self):
net['throat.cross_sectional_area'][[0, 1, 2]] = 0.3
net['pore.right'] = ~net['pore.left']
net.add_model(propname='pore.surface_area',
model=mods.circle,
domain='left',
regen_mode='normal')
model=mods.circle,
domain='left',
regen_mode='normal')
net.add_model(propname='pore.surface_area',
model=mods.circle,
domain='right',
regen_mode='normal')
a = np.array([2.84159265, 2.74159265, 2.74159265])
a = np.array([2.84159265, 2.54159265, 2.54159265])
b = net['pore.surface_area@left']
c = np.array([2.74159265, 2.74159265, 2.74159265, 2.94159265,
c = np.array([2.74159265, 2.94159265, 2.94159265, 2.94159265,
2.94159265, 2.94159265, 3.04159265])
d = net['pore.surface_area@right']
assert_allclose(a, b)
Expand Down
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