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
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')