def run(self, points=25, start=None, stop=None):
r"""
Runs the percolation algorithm to determine which pores and throats
will be invaded at each given pressure point.
Parameters
----------
points: int or array_like
An array containing the pressure points to apply. If a scalar is
given then an array will be generated with the given number of
points spaced between the lowest and highest values of
throat entry pressures using logarithmic spacing. To specify low
and high pressure points use the ``start`` and ``stop`` arguments.
start : int
The optional starting point to use when generating pressure points.
If not given the half the lowest capillary entry pressure in the
network is used.
stop : int
The optional stopping point to use when generating pressure points.
If not given, then twice the highest capillary entry pressure in
the network is used.
Notes
-----
The inlet sites are set to invaded to start the simulation. This means
that if 'internal' pores are used as inlets the capillary pressure
curve will begin at a non-zero invading phase saturation. To avoid
this either set the inlet pore volumes to zero or add boundary pores
to the inlet face, and set their volumes to zero.
"""
phase = self.project[self.settings.phase]
# Parse inputs and generate list of invasion points if necessary
if self.settings['mode'] == 'bond':
self['throat.entry_pressure'] = \
phase[self.settings['throat_entry_threshold']]
if start is None:
start = np.amin(self['throat.entry_pressure'])*0.5
if stop is None:
stop = np.amax(self['throat.entry_pressure'])*2.0
elif self.settings['mode'] == 'site':
self['pore.entry_pressure'] = \
phase[self.settings['pore_entry_threshold']]
if start is None:
start = np.amin(self['pore.entry_pressure'])*0.5
if stop is None:
stop = np.amax(self['pore.entry_pressure'])*2.0
else:
raise Exception('Percolation type has not been set')
if isinstance(points, int):
points = np.logspace(start=np.log10(max(1, start)),
stop=np.log10(stop), num=points)
self._points = points
# Ensure pore inlets have been set IF access limitations is True
if self.settings['access_limited']:
if np.sum(self['pore.inlets']) == 0:
raise Exception('Inlet pores must be specified first')
else:
Pin = self['pore.inlets']
# Generate curve from points
conns = self.project.network['throat.conns']
for inv_val in points:
if self.settings['mode'] == 'bond':
t_invaded = self['throat.entry_pressure'] <= inv_val
labels = bond_percolation(conns, t_invaded)
elif self.settings['mode'] == 'site':
p_invaded = self['pore.entry_pressure'] <= inv_val
labels = site_percolation(conns, p_invaded)
# Optionally remove clusters not connected to the inlets
if self.settings['access_limited']:
labels = remove_isolated_clusters(labels=labels,
inlets=Pin)
# Store current applied pressure in newly invaded pores
pinds = (self['pore.invasion_pressure'] == np.inf) * \
(labels.sites >= 0)
self['pore.invasion_pressure'][pinds] = inv_val
# Store current applied pressure in newly invaded throats
tinds = (self['throat.invasion_pressure'] == np.inf) * \
(labels.bonds >= 0)
self['throat.invasion_pressure'][tinds] = inv_val
# Convert invasion pressures in sequence values
Pinv = self['pore.invasion_pressure']
Tinv = self['throat.invasion_pressure']
Pseq = np.searchsorted(np.unique(Pinv), Pinv)
Tseq = np.searchsorted(np.unique(Tinv), Tinv)
self['pore.invasion_sequence'] = Pseq
self['throat.invasion_sequence'] = Tseq
def run(self, points=25, start=None, stop=None):
r"""
Runs the percolation algorithm to determine which pores and throats
will be invaded at each given pressure point.
Parameters
----------
points: int or array_like
An array containing the pressure points to apply. If a scalar is
given then an array will be generated with the given number of
points spaced between the lowest and highest values of
throat entry pressures using logarithmic spacing. To specify low
and high pressure points use the ``start`` and ``stop`` arguments.
start : int
The optional starting point to use when generating pressure points.
If not given the half the lowest capillary entry pressure in the
network is used.
stop : int
The optional stopping point to use when generating pressure points.
If not given, then twice the highest capillary entry pressure in
the network is used.
Note
----
The inlet sites are set to invaded to start the simulation. This means
that if 'internal' pores are used as inlets the capillary pressure
curve will begin at a non-zero invading phase saturation. To avoid
this either set the inlet pore volumes to zero or add boundary pores
to the inlet face, and set their volumes to zero.
"""
phase = self.project.find_phase(self)
# Parse inputs and generate list of invasion points if necessary
if self.settings['mode'] == 'bond':
self['throat.entry_pressure'] = \
phase[self.settings['throat_entry_threshold']]
if start is None:
start = sp.amin(self['throat.entry_pressure'])*0.5
if stop is None:
stop = sp.amax(self['throat.entry_pressure'])*2.0
elif self.settings['mode'] == 'site':
self['pore.entry_pressure'] = \
phase[self.settings['pore_entry_threshold']]
if start is None:
start = sp.amin(self['pore.entry_pressure'])*0.5
if stop is None:
stop = sp.amax(self['pore.entry_pressure'])*2.0
else:
raise Exception('Percolation type has not been set')
if type(points) is int:
points = sp.logspace(start=sp.log10(max(1, start)),
stop=sp.log10(stop), num=points)
self._points = points
# Ensure pore inlets have been set IF access limitations is True
if self.settings['access_limited']:
if sp.sum(self['pore.inlets']) == 0:
raise Exception('Inlet pores must be specified first')
else:
Pin = self['pore.inlets']
# Generate curve from points
conns = self.project.network['throat.conns']
for inv_val in points:
if self.settings['mode'] == 'bond':
t_invaded = self['throat.entry_pressure'] <= inv_val
labels = bond_percolation(conns, t_invaded)
elif self.settings['mode'] == 'site':
p_invaded = self['pore.entry_pressure'] <= inv_val
labels = site_percolation(conns, p_invaded)
# Optionally remove clusters not connected to the inlets
if self.settings['access_limited']:
labels = remove_isolated_clusters(labels=labels,
inlets=Pin)
# Store current applied pressure in newly invaded pores
pinds = (self['pore.invasion_pressure'] == sp.inf) * \
(labels.sites >= 0)
self['pore.invasion_pressure'][pinds] = inv_val
# Store current applied pressure in newly invaded throats
tinds = (self['throat.invasion_pressure'] == sp.inf) * \
(labels.bonds >= 0)
self['throat.invasion_pressure'][tinds] = inv_val
# Convert invasion pressures in sequence values
Pinv = self['pore.invasion_pressure']
Tinv = self['throat.invasion_pressure']
Pseq = sp.searchsorted(sp.unique(Pinv), Pinv)
Tseq = sp.searchsorted(sp.unique(Tinv), Tinv)
self['pore.invasion_sequence'] = Pseq
self['throat.invasion_sequence'] = Tseq