def __init__(self, network=None, phase=None, geometry=None,
pores=[], throats=[], **kwargs):
super().__init__(**kwargs)
logger.name = self.name
# Associate with Network
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
self._net._physics.append(self) # Register self with network
# Associate with Phase
if phase is None:
phase = GenericPhase(network=self._net)
phase._physics.append(self) # Register self with phase
self._phases.append(phase) # Register phase with self
if geometry is not None:
if (sp.size(pores) > 0) or (sp.size(throats) > 0):
raise Exception('Cannot specify a Geometry AND pores or throats')
pores = self._net.toindices(self._net['pore.' + geometry.name])
throats = self._net.toindices(self._net['throat.' + geometry.name])
# Initialize a label dictionary in the associated phase and network
self._phases[0]['pore.'+self.name] = False
self._phases[0]['throat.'+self.name] = False
self._net['pore.'+self.name] = False
self._net['throat.'+self.name] = False
try:
self.set_locations(pores=pores, throats=throats)
except:
self.controller.purge_object(self)
raise Exception('Provided locations are in use, instantiation cancelled')
def __init__(self, network=None, components=[], **kwargs):
super(GenericPhase, self).__init__(**kwargs)
logger.name = self.name
if network is None:
self._net = GenericNetwork()
else:
self._net = network
# Initialize label 'all' in the object's own info dictionaries
self['pore.all'] = self._net['pore.all']
self['throat.all'] = self._net['throat.all']
#Set standard conditions on the fluid to get started
self['pore.temperature'] = 298.0
self['pore.pressure'] = 101325.0
# Register Ohase object in Network dictionary
self._net['pore.' + self.name] = True
self._net['throat.' + self.name] = True
if components != []:
for comp in components:
self.set_component(phase=comp)
self._net._phases.append(self) # Append this Phase to the Network
def __init__(self,network=None,phase=None,geometry=None,pores=[],throats=[],**kwargs):
super(GenericPhysics,self).__init__(**kwargs)
logger.name = self.name
#Associate with Network
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
self._net._physics.append(self) # Register self with network
#Associate with Phase
if phase is None:
self._phases.append(GenericPhase())
else:
phase._physics.append(self) # Register self with phase
self._phases.append(phase) # Register phase with self
if geometry is not None:
if (pores != []) or (throats != []):
raise Exception('Cannot specify a Geometry AND pores or throats')
pores = self._net.toindices(self._net['pore.'+geometry.name])
throats = self._net.toindices(self._net['throat.'+geometry.name])
#Initialize a label dictionary in the associated fluid
self._phases[0]['pore.'+self.name] = False
self._phases[0]['throat.'+self.name] = False
self._net['pore.'+self.name] = False
self._net['throat.'+self.name] = False
self.set_locations(pores=pores,throats=throats)
def __init__(self, network=None, pores=[], throats=[], **kwargs):
super().__init__(**kwargs)
logger.name = self.name
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
# Register self with network.geometries
self._net._geometries.append(self)
# Initialize a label dictionary in the associated network
self._net['pore.' + self.name] = False
self._net['throat.' + self.name] = False
try:
self.set_locations(pores=pores, throats=throats)
except:
self.controller.purge_object(self)
raise Exception(
'Provided locations are in use, instantiation cancelled')
def __init__(self, network=None, **kwargs):
super().__init__(**kwargs)
logger.name = self.name
if network is None:
network = GenericNetwork()
self.network.update({network.name: network})
# Initialize label 'all' in the object's own info dictionaries
self['pore.all'] = self._net['pore.all']
self['throat.all'] = self._net['throat.all']
def __init__(self,
network=None,
phase=None,
geometry=None,
pores=[],
throats=[],
**kwargs):
super(GenericPhysics, self).__init__(**kwargs)
logger.name = self.name
#Associate with Network
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
self._net._physics.append(self) # Register self with network
#Associate with Phase
if phase is None:
self._phases.append(GenericPhase())
else:
phase._physics.append(self) # Register self with phase
self._phases.append(phase) # Register phase with self
if geometry is not None:
if (pores != []) or (throats != []):
raise Exception(
'Cannot specify a Geometry AND pores or throats')
pores = self._net.toindices(self._net['pore.' + geometry.name])
throats = self._net.toindices(self._net['throat.' + geometry.name])
#Initialize a label dictionary in the associated fluid
self._phases[0]['pore.' + self.name] = False
self._phases[0]['throat.' + self.name] = False
self._net['pore.' + self.name] = False
self._net['throat.' + self.name] = False
self.set_locations(pores=pores, throats=throats)
def __init__(self,
network=None,
pores=[],
throats=[],
seed=None,
**kwargs):
r"""
Initialize
"""
super(GenericGeometry, self).__init__(**kwargs)
logger.name = self.name
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
self._net._geometries.append(
self) # Register self with network.geometries
#Initialize a label dictionary in the associated network
self._net['pore.' + self.name] = False
self._net['throat.' + self.name] = False
self.set_locations(pores=pores, throats=throats)
self._seed = seed
def __init__(self,network=None,pores=[],throats=[],seed=None,**kwargs):
r"""
Initialize
"""
super(GenericGeometry,self).__init__(**kwargs)
logger.name = self.name
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
self._net._geometries.append(self) # Register self with network.geometries
#Initialize a label dictionary in the associated network
self._net['pore.'+self.name] = False
self._net['throat.'+self.name] = False
self.set_locations(pores=pores,throats=throats)
self._seed = seed
def __init__(self, network=None, pores=[], throats=[], **kwargs):
super().__init__(**kwargs)
logger.name = self.name
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
# Register self with network.geometries
self._net._geometries.append(self)
# Initialize a label dictionary in the associated network
self._net['pore.'+self.name] = False
self._net['throat.'+self.name] = False
try:
self.set_locations(pores=pores, throats=throats)
except:
self.controller.purge_object(self)
raise Exception('Provided locations are in use, instantiation cancelled')
def __init__(self, network=None, components=[], **kwargs):
super().__init__(**kwargs)
logger.name = self.name
if network is None:
network = GenericNetwork()
self.network.update({network.name: network})
# Initialize label 'all' in the object's own info dictionaries
self['pore.all'] = self._net['pore.all']
self['throat.all'] = self._net['throat.all']
# Set standard conditions on the fluid to get started
self['pore.temperature'] = 298.0
self['pore.pressure'] = 101325.0
# Register Ohase object in Network dictionary
self._net['pore.'+self.name] = True
self._net['throat.'+self.name] = True
if components != []:
for comp in components:
self.set_component(phase=comp)
self._net.phases.update({self.name: self}) # Connect Phase to Network
class GenericPhysics(OpenPNM.Base.Core):
r"""
Generic class to generate Physics objects
Parameters
----------
network : OpenPNM Network object
The network to which this Physics should be attached
phase : OpenPNM Phase object
The Phase object to which this Physics applies
geometry : OpenPNM Geometry object
The Geometry object that defines the pores/throats where this Physics
should be applied. If this argument is supplied, then pores and
throats cannot be specified.
pores and/or throats : array_like
The list of pores and throats where this physics applies. If either are
left blank this will apply the physics nowhere. The locations can be
change after instantiation using ``set_locations()``. If pores and
throats are supplied, than a geometry cannot be specified.
name : str, optional
A unique string name to identify the Physics object, typically same as
instance name but can be anything. If left blank, and name will be
generated that include the class name and a random string.
"""
def __init__(self,
network=None,
phase=None,
geometry=None,
pores=[],
throats=[],
**kwargs):
super(GenericPhysics, self).__init__(**kwargs)
logger.name = self.name
#Associate with Network
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
self._net._physics.append(self) # Register self with network
#Associate with Phase
if phase is None:
self._phases.append(GenericPhase())
else:
phase._physics.append(self) # Register self with phase
self._phases.append(phase) # Register phase with self
if geometry is not None:
if (pores != []) or (throats != []):
raise Exception(
'Cannot specify a Geometry AND pores or throats')
pores = self._net.toindices(self._net['pore.' + geometry.name])
throats = self._net.toindices(self._net['throat.' + geometry.name])
#Initialize a label dictionary in the associated fluid
self._phases[0]['pore.' + self.name] = False
self._phases[0]['throat.' + self.name] = False
self._net['pore.' + self.name] = False
self._net['throat.' + self.name] = False
self.set_locations(pores=pores, throats=throats)
def __getitem__(self, key):
element = key.split('.')[0]
# Convert self.name into 'all'
if key.split('.')[-1] == self.name:
key = element + '.all'
if key in self.keys(): # Look for data on self...
return super(GenericPhysics, self).__getitem__(key)
else: # ...Then check Network
return self._phases[0][key][self._phases[0][element + '.' +
self.name]]
def set_locations(self, pores=[], throats=[], mode='add'):
r'''
Set the pore and throat locations of the Physics object
Parameters
----------
pores and throats : array_like
The list of pores and/or throats where the object should be applied.
mode : string
Indicates whether list of pores or throats is to be added or removed
from the object. Options are 'add' (default) or 'remove'.
'''
if len(pores) > 0:
pores = sp.array(pores, ndmin=1)
self._set_locations(element='pore', locations=pores, mode=mode)
if len(throats) > 0:
throats = sp.array(throats, ndmin=1)
self._set_locations(element='throat', locations=throats, mode=mode)
class GenericGeometry(Core):
r"""
GenericGeometry - Base class to construct a Geometry object
Parameters
----------
network : OpenPNM Network Object
pores and/or throats : array_like
The list of pores and throats where this physics applies. If either are
left blank this will apply the physics nowhere. The locations can be
change after instantiation using ``set_locations()``.
name : string
A unique name to apply to the object. This name will also be used as a
label to identify where this this geometry applies.
Examples
--------
>>> pn = OpenPNM.Network.TestNet()
>>> Ps = pn.pores() # Get all pores
>>> Ts = pn.throats() # Get all throats
>>> geom = OpenPNM.Geometry.GenericGeometry(network=pn,pores=Ps,throats=Ts)
"""
def __init__(self,network=None,pores=[],throats=[],seed=None,**kwargs):
r"""
Initialize
"""
super(GenericGeometry,self).__init__(**kwargs)
logger.name = self.name
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
self._net._geometries.append(self) # Register self with network.geometries
#Initialize a label dictionary in the associated network
self._net['pore.'+self.name] = False
self._net['throat.'+self.name] = False
self.set_locations(pores=pores,throats=throats)
self._seed = seed
def __getitem__(self,key):
element = key.split('.')[0]
# Convert self.name into 'all'
if key.split('.')[-1] == self.name:
key = element + '.all'
if key in self.keys(): # Look for data on self...
return super(GenericGeometry,self).__getitem__(key)
if key == 'throat.conns': # Handle specifically
[P1,P2] = self._net['throat.conns'][self._net[element+'.'+self.name]].T
Pmap = sp.zeros((self._net.Np,),dtype=int)-1
Pmap[self._net.pores(self.name)] = self.Ps
conns = sp.array([Pmap[P1],Pmap[P2]]).T
# Replace -1's with nans
if sp.any(conns==-1):
conns = sp.array(conns,dtype=object)
conns[sp.where(conns==-1)] = sp.nan
return conns
else: # ...Then check Network
return self._net[key][self._net[element+'.'+self.name]]
def set_locations(self,pores=[],throats=[],mode='add'):
r'''
Set the pore and throat locations of the Geometry object
Parameters
----------
pores and throats : array_like
The list of pores and/or throats in the Network where the object
should be applied
mode : string
Indicates whether list of pores or throats is to be added or removed
from the object. Options are 'add' (default) or 'remove'.
'''
if len(pores) > 0:
pores = sp.array(pores,ndmin=1)
self._set_locations(element='pore',locations=pores,mode=mode)
if len(throats) > 0:
throats = sp.array(throats,ndmin=1)
self._set_locations(element='throat',locations=throats,mode=mode)
class GenericPhysics(OpenPNM.Base.Core):
r"""
Generic class to generate Physics objects
Parameters
----------
network : OpenPNM Network object
The network to which this Physics should be attached
phase : OpenPNM Phase object
The Phase object to which this Physics applies
geometry : OpenPNM Geometry object
The Geometry object that defines the pores/throats where this Physics
should be applied. If this argument is supplied, then pores and
throats cannot be specified.
pores and/or throats : array_like
The list of pores and throats where this physics applies. If either are
left blank this will apply the physics nowhere. The locations can be
change after instantiation using ``set_locations()``. If pores and
throats are supplied, than a geometry cannot be specified.
name : str, optional
A unique string name to identify the Physics object, typically same as
instance name but can be anything. If left blank, and name will be
generated that include the class name and a random string.
"""
def __init__(self, network=None, phase=None, geometry=None,
pores=[], throats=[], **kwargs):
super().__init__(**kwargs)
logger.name = self.name
# Associate with Network
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
self._net._physics.append(self) # Register self with network
# Associate with Phase
if phase is None:
phase = GenericPhase(network=self._net)
phase._physics.append(self) # Register self with phase
self._phases.append(phase) # Register phase with self
if geometry is not None:
if (sp.size(pores) > 0) or (sp.size(throats) > 0):
raise Exception('Cannot specify a Geometry AND pores or throats')
pores = self._net.toindices(self._net['pore.' + geometry.name])
throats = self._net.toindices(self._net['throat.' + geometry.name])
# Initialize a label dictionary in the associated phase and network
self._phases[0]['pore.'+self.name] = False
self._phases[0]['throat.'+self.name] = False
self._net['pore.'+self.name] = False
self._net['throat.'+self.name] = False
try:
self.set_locations(pores=pores, throats=throats)
except:
self.controller.purge_object(self)
raise Exception('Provided locations are in use, instantiation cancelled')
def __getitem__(self, key):
element = key.split('.')[0]
# Convert self.name into 'all'
if key.split('.')[-1] == self.name:
key = element + '.all'
if key in self.keys(): # Look for data on self...
return super(GenericPhysics, self).__getitem__(key)
else: # ...Then check Network
return self._phases[0][key][self._phases[0][element + '.' + self.name]]
def _set_phase(self, phase):
current_phase = self._phases[0]
# Remove labels of self from current phase
pore_label = current_phase.pop('pore.'+self.name)
throat_label = current_phase.pop('throat.'+self.name)
# Add labels of self to new phase
phase['pore.'+self.name] = pore_label
phase['throat.'+self.name] = throat_label
# Replace phase reference on self
self._phases[0] = phase
# Remove physics reference on current phase
current_phase._physics.remove(self)
phase._physics.append(self)
def _get_phase(self):
return self._phases[0]
parent_phase = property(fget=_get_phase, fset=_set_phase)
def set_locations(self, pores=[], throats=[], mode='add'):
r"""
Set the pore and throat locations of the Physics object
Parameters
----------
pores and throats : array_like
The list of pores and/or throats where the object should be applied.
mode : string
Indicates whether list of pores or throats is to be added or removed
from the object. Options are 'add' (default) or 'remove'.
"""
if sp.size(pores) > 0:
self._set_locations(element='pore', locations=pores, mode=mode)
if sp.size(throats) > 0:
self._set_locations(element='throat', locations=throats, mode=mode)
class GenericGeometry(Core):
r"""
GenericGeometry - Base class to construct a Geometry object
Parameters
----------
network : OpenPNM Network Object
pores and/or throats : array_like
The list of pores and throats where this physics applies. If either are
left blank this will apply the Geometry nowhere. The locations can be
changed after instantiation using ``set_locations()``.
name : string
A unique name to apply to the object. This name will also be used as a
label to identify where this geometry applies.
Examples
--------
>>> import OpenPNM
>>> pn = OpenPNM.Network.TestNet()
>>> Ps = pn.pores() # Get all pores
>>> Ts = pn.throats() # Get all throats
>>> geom = OpenPNM.Geometry.GenericGeometry(network=pn,
... pores=Ps,
... throats=Ts)
"""
def __init__(self, network=None, pores=[], throats=[], **kwargs):
super().__init__(**kwargs)
logger.name = self.name
if network is None:
self._net = GenericNetwork()
else:
self._net = network # Attach network to self
# Register self with network.geometries
self._net._geometries.append(self)
# Initialize a label dictionary in the associated network
self._net['pore.' + self.name] = False
self._net['throat.' + self.name] = False
try:
self.set_locations(pores=pores, throats=throats)
except:
self.controller.purge_object(self)
raise Exception(
'Provided locations are in use, instantiation cancelled')
def __getitem__(self, key):
element = key.split('.')[0]
# Convert self.name into 'all'
if key.split('.')[-1] == self.name:
key = element + '.all'
if key in list(self.keys()): # Look for data on self...
return super(GenericGeometry, self).__getitem__(key)
if key == 'throat.conns': # Handle specifically
[P1, P2] = \
self._net['throat.conns'][self._net[element+'.'+self.name]].T
Pmap = sp.zeros((self._net.Np, ), dtype=int) - 1
Pmap[self._net.pores(self.name)] = self.Ps
conns = sp.array([Pmap[P1], Pmap[P2]]).T
# Replace -1's with nans
if sp.any(conns == -1):
conns = sp.array(conns, dtype=object)
conns[sp.where(conns == -1)] = sp.nan
return conns
else: # ...Then check Network
return self._net[key][self._net[element + '.' + self.name]]
def set_locations(self, pores=[], throats=[], mode='add'):
r"""
Set the pore and throat locations of the Geometry object
Parameters
----------
pores and throats : array_like
The list of pores and/or throats in the Network where the object
should be applied
mode : string
Indicates whether list of pores or throats is to be added or
removed from the object. Options are 'add' (default) or 'remove'.
"""
if sp.size(pores) > 0:
self._set_locations(element='pore', locations=pores, mode=mode)
if sp.size(throats) > 0:
self._set_locations(element='throat', locations=throats, mode=mode)
def plot_histograms(self,
throat_diameter='throat.diameter',
pore_diameter='pore.diameter',
throat_length='throat.length'):
Plots.distributions(obj=self,
throat_diameter=throat_diameter,
pore_diameter=pore_diameter,
throat_length=throat_length)
plot_histograms.__doc__ = Plots.distributions.__doc__
