def set_residual(self, pores=[], overwrite=False):
r"""
Method to start invasion in a network w. residual saturation.
Called after inlets are set.
Parameters
----------
pores : array_like
The pores locations that are to be filled with invader at the
beginning of the simulation.
overwrite : boolean
If ``True`` then all existing inlet locations will be removed and
then the supplied locations will be added. If ``False``, then
supplied locations are added to any already existing locations.
Notes
-----
Currently works for pores only and treats inner throats, i.e.
those that connect two pores in the cluster as invaded and outer ones
as uninvaded. Uninvaded throats are added to a new residual cluster
queue but do not start invading independently if not connected to an
inlet.
Step 1. Identify clusters in the phase occupancy.
Step 2. Look for clusters that are connected or contain an inlet
Step 3. For those that are merge into inlet cluster. May be connected
to more than one - run should sort this out
Step 4. For those that are isolated set the queue to not invading.
Step 5. (in run) When isolated cluster is met my invading cluster it
merges in and starts invading
"""
Ps = self._parse_indices(pores)
if overwrite:
self['pore.residual'] = False
self['pore.residual'][Ps] = True
residual = self['pore.residual']
net = self.project.network
conns = net['throat.conns']
rclusters = site_percolation(conns, residual).sites
rcluster_ids = np.unique(rclusters[rclusters > -1])
initial_num = len(self.queue)-1
for rcluster_id in rcluster_ids:
rPs = rclusters == rcluster_id
existing = np.unique(self['pore.cluster'][rPs])
existing = existing[existing > -1]
if len(existing) > 0:
# There was at least one inlet cluster connected to this
# residual cluster, pick the first one.
cluster_num = existing[0]
else:
# Make a new cluster queue
cluster_num = len(self.queue)
self.queue.append([])
queue = self.queue[cluster_num]
# Set the residual pores and inner throats as part of cluster
self['pore.cluster'][rPs] = cluster_num
Ts = net.find_neighbor_throats(pores=rPs,
flatten=True,
mode='xnor')
self['throat.cluster'][Ts] = cluster_num
self['pore.invasion_sequence'][rPs] = 0
self['throat.invasion_sequence'][Ts] = 0
self['pore.invasion_pressure'][rPs] = -np.inf
self['throat.invasion_pressure'][Ts] = -np.inf
# Add all the outer throats to the queue
Ts = net.find_neighbor_throats(pores=rPs,
flatten=True,
mode='exclusive_or')
for T in Ts:
data = []
# Pc
data.append(self['throat.entry_pressure'][T])
# Element Index
data.append(T)
# Element Type (Pore of Throat)
data.append('throat')
hq.heappush(queue, data)
self.invasion_running = [True]*len(self.queue)
# we have added new clusters that are currently isolated and we
# need to stop them invading until they merge into an invading
# cluster
for c_num in range(len(self.queue)):
if c_num > initial_num:
self.invasion_running[c_num] = False
def set_residual(self, pores=[], overwrite=False):
r"""
Method to start invasion in a network w. residual saturation.
Called after inlets are set.
Parameters
----------
pores : array_like
The pores locations that are to be filled with invader at the
beginning of the simulation.
overwrite : boolean
If ``True`` then all existing inlet locations will be removed and
then the supplied locations will be added. If ``False``, then
supplied locations are added to any already existing locations.
Notes
-----
Currently works for pores only and treats inner throats, i.e.
those that connect two pores in the cluster as invaded and outer ones
as uninvaded. Uninvaded throats are added to a new residual cluster
queue but do not start invading independently if not connected to an
inlet.
Step 1. Identify clusters in the phase occupancy.
Step 2. Look for clusters that are connected or contain an inlet
Step 3. For those that are merge into inlet cluster. May be connected
to more than one - run should sort this out
Step 4. For those that are isolated set the queue to not invading.
Step 5. (in run) When isolated cluster is met my invading cluster it
merges in and starts invading
"""
Ps = self._parse_indices(pores)
if overwrite:
self['pore.residual'] = False
self['pore.residual'][Ps] = True
residual = self['pore.residual']
net = self.project.network
conns = net['throat.conns']
rclusters = site_percolation(conns, residual).sites
rcluster_ids = np.unique(rclusters[rclusters > -1])
initial_num = len(self.queue)-1
for rcluster_id in rcluster_ids:
rPs = rclusters == rcluster_id
existing = np.unique(self['pore.cluster'][rPs])
existing = existing[existing > -1]
if len(existing) > 0:
# There was at least one inlet cluster connected to this
# residual cluster, pick the first one.
cluster_num = existing[0]
else:
# Make a new cluster queue
cluster_num = len(self.queue)
self.queue.append([])
queue = self.queue[cluster_num]
# Set the residual pores and inner throats as part of cluster
self['pore.cluster'][rPs] = cluster_num
Ts = net.find_neighbor_throats(pores=rPs,
flatten=True,
mode='xnor')
self['throat.cluster'][Ts] = cluster_num
self['pore.invasion_sequence'][rPs] = 0
self['throat.invasion_sequence'][Ts] = 0
self['pore.invasion_pressure'][rPs] = -np.inf
self['throat.invasion_pressure'][Ts] = -np.inf
# Add all the outer throats to the queue
Ts = net.find_neighbor_throats(pores=rPs,
flatten=True,
mode='exclusive_or')
for T in Ts:
data = []
# Pc
data.append(self['throat.entry_pressure'][T])
# Element Index
data.append(T)
# Element Type (Pore of Throat)
data.append('throat')
hq.heappush(queue, data)
self.invasion_running = [True]*len(self.queue)
# we have added new clusters that are currently isolated and we
# need to stop them invading until they merge into an invading
# cluster
for c_num in range(len(self.queue)):
if c_num > initial_num:
self.invasion_running[c_num] = False
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
