def __init__(self,
shapes,
spacings,
origins,
labels=None,
name=None,
project=None):
# If no labels given, then use default
if labels is None:
labels = [None for i in shapes]
# Generate cubic networks of specified properties and store in a list
nets = []
for n in range(len(shapes)):
net = Cubic(shape=shapes[n], spacing=spacings[n], name=labels[n])
# label_faces(net)
net['pore.coords'] += origins[n]
nets.append(net)
# Begin the process of merging the networks, but no stitching yet
main_net = nets.pop(0)
for net in nets:
extend(network=main_net,
pore_coords=net['pore.coords'],
throat_conns=net['throat.conns'] + main_net.Np)
for net in nets:
P1 = main_net.pores('surface')
P1 = net.pores('surface')
stitch(network=main_net)
def __init__(self, shapes, spacings, origins, labels=None, name=None,
project=None):
# If no labels given, then use default
if labels is None:
labels = [None for i in shapes]
# Generate cubic networks of specified properties and store in a list
nets = []
for n in range(len(shapes)):
net = Cubic(shape=shapes[n], spacing=spacings[n], name=labels[n])
# label_faces(net)
net['pore.coords'] += origins[n]
nets.append(net)
# Begin the process of merging the networks, but no stitching yet
main_net = nets.pop(0)
for net in nets:
extend(network=main_net, pore_coords=net['pore.coords'],
throat_conns=net['throat.conns'] + main_net.Np)
for net in nets:
P1 = main_net.pores('surface')
P1 = net.pores('surface')
stitch(network=main_net)
def __init__(self, shape, name=None, **kwargs):
super().__init__(name=name)
net = Cubic(shape=shape,
spacing=1e-4,
connectivity=26,
project=self,
**kwargs)
geom = GenericGeometry(network=net, pores=net.Ps, throats=net.Ts)
geom.add_model(propname='pore.seed',
model=gm.pore_seed.spatially_correlated,
weights=[1, 1, 1])
geom.add_model(propname='pore.diameter',
model=gm.pore_size.weibull,
shape=2.2,
scale=2e-5,
loc=1e-6)
geom.add_model(propname='pore.volume', model=gm.pore_volume.sphere)
geom.add_model(propname='throat.length',
model=gm.throat_length.spheres_and_cylinders)
geom.add_model(propname='throat.diameter',
model=gm.throat_size.from_neighbor_pores,
prop='pore.diameter',
mode='min')
geom.add_model(propname='throat.volume',
model=gm.throat_volume.cylinder)
geom.regenerate_models()
def __init__(self,
shape,
spacing=1,
label_1='primary',
label_2='secondary',
**kwargs):
super().__init__(**kwargs)
spacing = sp.array(spacing)
shape = sp.array(shape)
# Deal with non-3D shape arguments
shape = sp.pad(shape, [0, 3 - shape.size],
mode='constant',
constant_values=1)
net = Cubic(shape=shape, spacing=1)
net['throat.' + label_1] = True
net['pore.' + label_1] = True
single_dim = shape == 1
shape[single_dim] = 2
dual = Cubic(shape=shape - 1, spacing=1)
faces = [['front', 'back'], ['left', 'right'], ['top', 'bottom']]
faces = [faces[i] for i in sp.where(~single_dim)[0]]
faces = sp.array(faces).flatten().tolist()
dual.add_boundary_pores(faces)
# Add secondary network name as a label
dual['pore.' + label_2] = True
dual['throat.' + label_2] = True
# Shift coordinates prior to stitching
dual['pore.coords'] += 0.5 * (~single_dim)
topotools.stitch(net,
dual,
P_network=net.Ps,
P_donor=dual.Ps,
len_max=1)
net['throat.interconnect'] = net['throat.stitched']
del net['throat.stitched']
# Clean-up labels
net['pore.surface'] = False
net['throat.surface'] = False
for face in faces:
# Remove face label from secondary network since it's internal now
Ps = net.pores(labels=[face, label_2], mode='xnor')
net['pore.' + face][Ps] = False
Ps = net.pores(labels=[face + '_boundary'])
net['pore.' + face][Ps] = True
Ps = net.pores(face)
net['pore.surface'][Ps] = True
Ts = net.find_neighbor_throats(pores=Ps, mode='xnor')
net['throat.surface'][Ts] = True
net['throat.' + face] = net.tomask(throats=Ts)
[net.pop(item) for item in net.labels() if 'boundary' in item]
# Label non-surface pores and throats as internal
net['pore.internal'] = True
net['throat.internal'] = True
# Transfer all dictionary items from 'net' to 'self'
[self.update({item: net[item]}) for item in net]
ws.close_project(net.project)
# Finally, scale network to requested spacing
net['pore.coords'] *= spacing
""" import openpnm as op from openpnm.network import Cubic from openpnm.phases import Air, Water, MultiPhase from openpnm.geometry import SpheresAndCylinders from openpnm.physics import Standard from openpnm.models.misc import constant from openpnm.models.physics.source_terms import linear import matplotlib.pyplot as plt import numpy as np np.random.seed(10) # Define network, geometry and constituent phases shape = np.array([100, 100, 1]) net = Cubic(shape=shape) geom = StickAndBall(network=net, pores=net.Ps, throats=net.Ts) air = Air(network=net, name="air") water = Water(network=net, name="water") water["pore.diffusivity"] = air["pore.diffusivity"] * 0.05 # Define the regions to be occupied by the two phases (air and water) x, y, z = net["pore.coords"].T ps_water = net.Ps[(y >= 75) + (y <= 25)] ps_air = np.setdiff1d(net.Ps, ps_water) ts_water = net.find_neighbor_throats(pores=ps_water, mode="xnor") ts_air = net.find_neighbor_throats(pores=ps_air, mode="xnor") ts_interface = net.find_neighbor_throats(pores=ps_water, mode="xor") # Define multiphase and set phase occupancy mphase = MultiPhase(network=net, phases=[air, water], name="mphase")
def __init__(self, shape, mode='sc', spacing=1, **kwargs):
super().__init__(**kwargs)
shape = np.array(shape)
if np.any(shape < 2):
raise Exception('Bravais lattice networks must have at least 2 '
'pores in all directions')
if mode == 'bcc':
# Make a basic cubic for the coner pores
net1 = Cubic(shape=shape)
net1['pore.net1'] = True
# Create a smaller cubic for the body pores, and shift it
net2 = Cubic(shape=shape - 1)
net2['pore.net2'] = True
net2['pore.coords'] += 0.5
# Stitch them together
topotools.stitch(net1, net2, net1.Ps, net2.Ps, len_max=0.99)
self.update(net1)
ws.close_project(net1.project)
# Deal with labels
Ps1 = self['pore.net2']
self.clear(mode='labels')
self['pore.corner_sites'] = ~Ps1
self['pore.body_sites'] = Ps1
Ts = self.find_neighbor_throats(pores=self.pores('body_sites'),
mode='exclusive_or')
self['throat.corner_to_body'] = False
self['throat.corner_to_body'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('corner_sites'),
mode='xnor')
self['throat.corner_to_corner'] = False
self['throat.corner_to_corner'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('body_sites'),
mode='xnor')
self['throat.body_to_body'] = False
self['throat.body_to_body'][Ts] = True
elif mode == 'fcc':
shape = np.array(shape)
# Create base cubic network of corner sites
net1 = Cubic(shape=shape)
# Create 3 networks to become face sites
net2 = Cubic(shape=shape - [1, 1, 0])
net3 = Cubic(shape=shape - [1, 0, 1])
net4 = Cubic(shape=shape - [0, 1, 1])
net2['pore.coords'] += np.array([0.5, 0.5, 0])
net3['pore.coords'] += np.array([0.5, 0, 0.5])
net4['pore.coords'] += np.array([0, 0.5, 0.5])
# Remove throats from net2 (trim doesn't work when removing ALL)
for n in [net2, net3, net4]:
n.clear(element='throat', mode='all')
n.update({'throat.all': np.array([], dtype=bool)})
n.update({'throat.conns': np.ndarray([0, 2], dtype=bool)})
# Join networks 2, 3 and 4 into one with all face sites
topotools.stitch(net2,
net3,
net2.Ps,
net3.Ps,
method='radius',
len_max=0.75)
topotools.stitch(net2,
net4,
net2.Ps,
net4.Ps,
method='radius',
len_max=0.75)
# Join face sites network with the corner sites network
topotools.stitch(net1,
net2,
net1.Ps,
net2.Ps,
method='radius',
len_max=0.75)
self.update(net1)
ws.close_project(net1.project)
# Deal with labels
self.clear(mode='labels')
Ps = np.any(np.mod(self['pore.coords'], 1) == 0, axis=1)
self['pore.face_sites'] = Ps
self['pore.corner_sites'] = ~Ps
Ts = self.find_neighbor_throats(pores=self.pores('corner_sites'),
mode='xnor')
self['throat.corner_to_corner'] = False
self['throat.corner_to_corner'][Ts] = True
Ts = self.find_neighbor_throats(pores=self.pores('face_sites'))
self['throat.corner_to_face'] = False
self['throat.corner_to_face'][Ts] = True
elif mode == 'hcp':
raise NotImplementedError('hcp is not implemented yet')
elif mode == 'sc':
net = Cubic(shape=shape, spacing=1)
self.update(net)
ws.close_project(net.project)
self.clear(mode='labels')
self['pore.corner_sites'] = True
self['throat.corner_to_corner'] = True
else:
raise Exception('Unrecognized lattice type: ' + mode)
# Finally scale network to specified spacing
topotools.label_faces(self)
Ps = self.pores(['left', 'right', 'top', 'bottom', 'front', 'back'])
Ps = self.to_mask(pores=Ps)
self['pore.surface'] = Ps
self['pore.coords'] *= np.array(spacing)
def __init__(self,
shape,
spacing=1.0,
length=1.0,
psd_params={'distribution': 'norm',
'loc': None,
'scale': None},
name=None,
settings={},
**kwargs):
super().__init__(name=name)
self.settings.update(defsets)
self.settings.update(settings)
if isinstance(shape, int):
shape = sp.array([shape, shape, 2])
elif len(shape) == 2:
shape = sp.concatenate((sp.array(shape), [2]))
else:
raise Exception('shape not understood, must be int ' +
' or list of 2 ints')
if isinstance(spacing, float) or isinstance(spacing, int):
spacing = float(spacing)
self.settings['spacing'] = spacing
spacing = sp.array([spacing, spacing, length])
else:
raise Exception('spacing not understood, must be float')
net = Cubic(shape=shape, spacing=spacing, project=self, **kwargs)
Ps_top = net.pores('top')
Ps_bot = net.pores('bottom')
Ts = net.find_connecting_throat(P1=Ps_top, P2=Ps_bot)
Ts = net.tomask(throats=Ts)
trim(network=net, throats=~Ts)
geom = GenericGeometry(network=net, pores=net.Ps, throats=net.Ts)
geom.add_model(propname='throat.seed',
model=mods.geometry.throat_seed.random)
if psd_params['loc'] is None:
psd_params['loc'] = spacing[0]/2
if psd_params['scale'] is None:
psd_params['scale'] = spacing[0]/10
if psd_params['distribution'] in ['norm', 'normal', 'gaussian']:
geom.add_model(propname='throat.size_distribution',
seeds='throat.seed',
model=mods.geometry.throat_size.normal,
loc=psd_params['loc'], scale=psd_params['scale'])
elif psd_params['distribution'] in ['weibull']:
geom.add_model(propname='throat.size_distribution',
seeds='throat.seed',
model=mods.geometry.throat_size.weibull,
loc=psd_params['loc'],
scale=psd_params['scale'],
shape=psd_params['shape'])
else:
temp = psd_params.copy()
func = getattr(spst, temp.pop('distribution'))
psd = func.freeze(**temp)
geom.add_model(propname='throat.size_distribution',
seeds='throat.seed',
model=mods.geometry.throat_size.generic_distribution,
func=psd)
if sp.any(geom['throat.size_distribution'] < 0):
logger.warning('Given size distribution produced negative ' +
'throat diameters...these will be set to 0')
geom.add_model(propname='throat.diameter',
model=mods.misc.clip,
prop='throat.size_distribution',
xmin=1e-12, xmax=sp.inf)
if self.settings['adjust_psd'] is None:
if geom['throat.size_distribution'].max() > spacing[0]:
logger.warning('Given size distribution produced throats ' +
'larger than the spacing.')
elif self.settings['adjust_psd'] == 'clip':
geom.add_model(propname='throat.diameter',
model=mods.misc.clip,
prop='throat.size_distribution',
xmin=1e-12, xmax=spacing[0])
if geom['throat.size_distribution'].max() > spacing[0]:
logger.warning('Given size distribution produced throats ' +
'larger than the spacing...tube diameters ' +
'will be clipped between 0 and given spacing')
elif self.settings['adjust_psd'] == 'normalize':
tmin = max(1e-12, geom['throat.size_distribution'].min())
geom.add_model(propname='throat.diameter',
model=mods.misc.normalize,
prop='throat.size_distribution',
xmin=tmin, xmax=spacing[0])
if geom['throat.size_distribution'].max() > spacing[0]:
logger.warning('Given size distribution produced throats ' +
'larger than the spacing...tube diameters ' +
'will be normalized to fit given spacing')
else:
logger.warning('Settings not understood, ignoring')
geom.add_model(propname='pore.diameter',
model=mods.geometry.pore_size.from_neighbor_throats,
throat_prop='throat.diameter', mode='max')
geom.add_model(propname='pore.diameter',
model=mods.misc.constant, value=0.0)
geom.add_model(propname='throat.length',
model=mods.geometry.throat_length.ctc)
geom.add_model(propname='throat.area',
model=mods.geometry.throat_area.cylinder)
geom.add_model(propname='pore.area',
model=mods.misc.from_neighbor_throats,
throat_prop='throat.area')
geom.add_model(propname='pore.volume',
model=mods.misc.constant, value=0.0)
geom.add_model(propname='throat.volume',
model=mods.geometry.throat_volume.cylinder)
geom.regenerate_models()
# Now create a generic phase with physics models on it
phase = GenericPhase(network=net)
m = mods.physics.hydraulic_conductance.classic_hagen_poiseuille
phase.add_model(propname='throat.hydraulic_conductance',
model=m, regen_mode='deferred')
m = mods.physics.diffusive_conductance.classic_ordinary_diffusion
phase.add_model(propname='throat.diffusive_conductance',
model=m, regen_mode='deferred')
m = mods.physics.diffusive_conductance.classic_ordinary_diffusion
phase.add_model(propname='throat.entry_pressure',
model=m, regen_mode='deferred')
def __init__(self,
shape,
spacing=1.0,
length=1.0,
psd_params={
'distribution': 'norm',
'loc': None,
'scale': None
},
name=None,
settings={},
**kwargs):
super().__init__(name=name)
self.settings.update(defsets)
self.settings.update(settings)
if isinstance(shape, int):
shape = sp.array([shape, shape, 2])
elif len(shape) == 2:
shape = sp.concatenate((sp.array(shape), [2]))
else:
raise Exception('shape not understood, must be int ' +
' or list of 2 ints')
if isinstance(spacing, float) or isinstance(spacing, int):
spacing = float(spacing)
self.settings['spacing'] = spacing
spacing = sp.array([spacing, spacing, length])
else:
raise Exception('spacing not understood, must be float')
net = Cubic(shape=shape, spacing=spacing, project=self, **kwargs)
Ps_top = net.pores('top')
Ps_bot = net.pores('bottom')
Ts = net.find_connecting_throat(P1=Ps_top, P2=Ps_bot)
Ts = net.tomask(throats=Ts)
trim(network=net, throats=~Ts)
geom = GenericGeometry(network=net, pores=net.Ps, throats=net.Ts)
geom.add_model(propname='throat.seed',
model=mods.geometry.throat_seed.random)
if psd_params['loc'] is None:
psd_params['loc'] = spacing[0] / 2
if psd_params['scale'] is None:
psd_params['scale'] = spacing[0] / 10
if psd_params['distribution'] in ['norm', 'normal', 'gaussian']:
geom.add_model(propname='throat.size_distribution',
seeds='throat.seed',
model=mods.geometry.throat_size.normal,
loc=psd_params['loc'],
scale=psd_params['scale'])
elif psd_params['distribution'] in ['weibull']:
geom.add_model(propname='throat.size_distribution',
seeds='throat.seed',
model=mods.geometry.throat_size.weibull,
loc=psd_params['loc'],
scale=psd_params['scale'],
shape=psd_params['shape'])
else:
temp = psd_params.copy()
func = getattr(spst, temp.pop('distribution'))
psd = func.freeze(**temp)
geom.add_model(
propname='throat.size_distribution',
seeds='throat.seed',
model=mods.geometry.throat_size.generic_distribution,
func=psd)
if sp.any(geom['throat.size_distribution'] < 0):
logger.warning('Given size distribution produced negative ' +
'throat diameters...these will be set to 0')
geom.add_model(propname='throat.diameter',
model=mods.misc.clip,
prop='throat.size_distribution',
xmin=1e-12,
xmax=sp.inf)
if self.settings['adjust_psd'] is None:
if geom['throat.size_distribution'].max() > spacing[0]:
logger.warning('Given size distribution produced throats ' +
'larger than the spacing.')
elif self.settings['adjust_psd'] == 'clip':
geom.add_model(propname='throat.diameter',
model=mods.misc.clip,
prop='throat.size_distribution',
xmin=1e-12,
xmax=spacing[0])
if geom['throat.size_distribution'].max() > spacing[0]:
logger.warning('Given size distribution produced throats ' +
'larger than the spacing...tube diameters ' +
'will be clipped between 0 and given spacing')
elif self.settings['adjust_psd'] == 'normalize':
tmin = max(1e-12, geom['throat.size_distribution'].min())
geom.add_model(propname='throat.diameter',
model=mods.misc.normalize,
prop='throat.size_distribution',
xmin=tmin,
xmax=spacing[0])
if geom['throat.size_distribution'].max() > spacing[0]:
logger.warning('Given size distribution produced throats ' +
'larger than the spacing...tube diameters ' +
'will be normalized to fit given spacing')
else:
logger.warning('Settings not understood, ignoring')
geom.add_model(propname='pore.diameter',
model=mods.geometry.pore_size.from_neighbor_throats,
throat_prop='throat.diameter',
mode='max')
geom.add_model(propname='pore.diameter',
model=mods.misc.constant,
value=0.0)
geom.add_model(propname='throat.length',
model=mods.geometry.throat_length.ctc)
geom.add_model(propname='throat.area',
model=mods.geometry.throat_area.cylinder)
geom.add_model(propname='pore.area',
model=mods.misc.from_neighbor_throats,
throat_prop='throat.area')
geom.add_model(propname='pore.volume',
model=mods.misc.constant,
value=0.0)
geom.add_model(propname='throat.volume',
model=mods.geometry.throat_volume.cylinder)
geom.regenerate_models()
# Now create a generic phase with physics models on it
phase = GenericPhase(network=net)
m = mods.physics.hydraulic_conductance.classic_hagen_poiseuille
phase.add_model(propname='throat.hydraulic_conductance',
model=m,
regen_mode='deferred')
m = mods.physics.diffusive_conductance.classic_ordinary_diffusion
phase.add_model(propname='throat.diffusive_conductance',
model=m,
regen_mode='deferred')
m = mods.physics.diffusive_conductance.classic_ordinary_diffusion
phase.add_model(propname='throat.entry_pressure',
model=m,
regen_mode='deferred')