def domain_length(self, face_1, face_2):
r"""
Returns the distance between two faces
No coplanar checking this is done in vertex_dimension
"""
L = vo.vertex_dimension(self, face_1, face_2, parm='length')
return L
def domain_length(self, face_1, face_2):
r"""
Returns the distance between two faces
No coplanar checking this is done in vertex_dimension
"""
L = vo.vertex_dimension(self, face_1, face_2, parm='length')
return L
def test_simple_cubic(self):
pn = OpenPNM.Network.DelaunayCubic(shape=[3, 3, 3])
pn.add_boundaries()
B1 = pn.pores("top_boundary")
B2 = pn.pores("bottom_boundary")
assert vo.vertex_dimension(pn, B1, B2, 'minmax') == [0.0, 3.0, 0.0,
3.0, 0.0, 3.0]
assert pn.num_pores() == 81
def domain_area(self, face):
r"""
Returns the area of a face
No coplanar checking this is done in vertex_dimension
"""
A = vo.vertex_dimension(self, face, parm='area')
return A
def domain_area(self, face):
r"""
Returns the area of a face
No coplanar checking this is done in vertex_dimension
"""
A = vo.vertex_dimension(self, face, parm='area')
return A
def domain_area(self,face):
r"""
Returns the area of a face
No coplanar checking this is done in vertex_dimension
Example
--------
>>> import OpenPNM
>>> pn = OpenPNM.Network.Delaunay(num_pores=100, domain_size=[3,2,1])
>>> pn.add_boundaries()
>>> B1 = pn.pores("left_boundary")
>>> B2 = pn.pores("right_boundary")
>>> pn.domain_area(B1)
3.0
"""
A = vo.vertex_dimension(self,face,parm='area')
return A
def domain_length(self,face_1,face_2):
r"""
Returns the distance between two faces
No coplanar checking this is done in vertex_dimension
Example
--------
>>> import OpenPNM
>>> pn = OpenPNM.Network.Delaunay(num_pores=100, domain_size=[3,2,1])
>>> pn.add_boundaries()
>>> B1 = pn.pores("left_boundary")
>>> B2 = pn.pores("right_boundary")
>>> pn.domain_length(B1,B2)
2.0
"""
L = vo.vertex_dimension(self,face_1,face_2,parm='length')
return L
def _calc_eff_prop(self, check_health=False):
r"""
This returns the main parameters for calculating the effective
property in a linear transport equation.
It also checks for the proper boundary conditions, inlets and outlets.
Parameters
----------
check_health : boolean(optional)
It analyzes the inlet and outlet pores to check their spatial
positions
"""
try:
self[self._quantity]
except KeyError:
raise Exception('The algorithm has not been run yet. Cannot ' +
'calculate effective property.')
# Determine boundary conditions by analyzing algorithm object
Ps = self.pores('pore.Dirichlet')
BCs = sp.unique(self['pore.bcval_Dirichlet'][Ps])
if sp.shape(BCs)[0] != 2:
raise Exception('The supplied algorithm did not have appropriate' +
' BCs')
inlets = sp.where(self['pore.' +
'bcval_Dirichlet'] == sp.amax(BCs))[0]
outlets = sp.where(self['pore.' +
'bcval_Dirichlet'] == sp.amin(BCs))[0]
# Analyze input and output pores
if check_health:
# Check for coplanarity
if self._net.iscoplanar(inlets) is False:
raise Exception('The inlet pores do not define a plane. ' +
'Effective property will be approximation')
if self._net.iscoplanar(outlets) is False:
raise Exception('The outlet pores do not define a plane. ' +
'Effective property will be approximation')
# Ensure pores are on a face of domain
# (only 1 non-self neighbor each)
PnI = self._net.find_neighbor_pores(pores=inlets,
mode='not_intersection',
excl_self=True)
if sp.shape(PnI) != sp.shape(inlets):
logger.warning('The inlet pores have too many neighbors. ' +
'Internal pores appear to be selected.')
pass
PnO = self._net.find_neighbor_pores(pores=outlets,
mode='not_intersection',
excl_self=True)
if sp.shape(PnO) != sp.shape(outlets):
logger.warning('The outlet pores have too many neighbors. ' +
'Internal pores appear to be selected.')
pass
# Fetch area and length of domain
if 'pore.vert_index' in self._net.props():
A = vo.vertex_dimension(network=self._net, face1=inlets,
parm='area')
L = vo.vertex_dimension(network=self._net, face1=inlets,
face2=outlets, parm='length')
else:
A = self._net.domain_area(face=inlets)
L = self._net.domain_length(face_1=inlets, face_2=outlets)
flow = self.rate(pores=inlets)
D = sp.sum(flow)*L/A/(BCs[0] - BCs[1])
return D
def add_boundaries(self):
r"""
This method identifies pores in the original Voronoi object that straddle a
boundary imposed by the reflection. The pore inside the original set of pores
(with index 0 - Np) is identified and the coordinates are saved. The vertices
making up the boundary throat are retrieved from the ridge_dict values and
these are used to identify which boundary the throat sits at.
A new pore and new connection is created with coordinates lying on the
boundary plane.
N.B This method will only work properly if the original network remains
unaltered i.e. not trimmed or extended
This preserves the connection between pore index on the network object
and the Voronoi object
The point of using this method is so that the throat vertices created by
the Voronoi object are preserved
This method will create boundary pores at the centre of the voronoi faces
that align with the outer planes of the domain.
The original pores in the domain are labelled internal and the boundary pores
are labelled external
Examples
--------
>>> import OpenPNM
>>> pn = OpenPNM.Network.Delaunay(num_pores=100,
... domain_size=[0.0001,0.0001,0.0001])
>>> pn.add_boundaries()
>>> pn.num_pores('boundary') > 0
True
"""
bound_conns = []
bound_coords = []
bound_vert_index = []
throat_vert_index = []
# Find boundary extent
[x_min, x_max, y_min, y_max, z_min, z_max] = \
vo.vertex_dimension(self, self.pores(), parm='minmax')
min_point = np.around(np.array([x_min, y_min, z_min]), 10)
max_point = np.around(np.array([x_max, y_max, z_max]), 10)
Np = self.num_pores()
Nt = self.num_throats()
new_throat_count = 0
# ridge_dict contains a dictionary where the key is a set of 2 neighbouring
# pores and the value is the vertex indices that form the throat or ridge
# between them
for p, v in self._vor.ridge_dict.items():
# If the vertex with index -1 is contained in list then the ridge is
# unbounded - ignore these
if np.all(np.asarray(v) >= 0):
# Boundary throats will be those connecting one pore inside the
# original set and one out
if (p[0] in range(Np) and p[1] not in range(Np)) or \
(p[0] not in range(Np) and p[1] in range(Np)):
# The dictionary key is not in numerical order so find the pore
# index inside
if p[0] in range(Np):
my_pore = p[0]
else:
my_pore = p[1]
my_pore_coord = self["pore.coords"][my_pore]
new_pore_coord = my_pore_coord.copy()
# Rounding necessary here to identify the plane as Voronoi can
# have 1e-17 and smaller errors
throat_verts = np.around(self._vor.vertices[v], 10)
# Find which plane we are aligned with (if any) and align
# new_pore with throat plane
if len(np.unique(throat_verts[:, 0])) == 1:
new_pore_coord[0] = np.unique(throat_verts[:, 0])
elif len(np.unique(throat_verts[:, 1])) == 1:
new_pore_coord[1] = np.unique(throat_verts[:, 1])
elif len(np.unique(throat_verts[:, 2])) == 1:
new_pore_coord[2] = np.unique(throat_verts[:, 2])
else:
new_pore_coord = np.mean(throat_verts, axis=0)
pass
bound_coords.append(new_pore_coord)
bound_conns.append(
np.array([my_pore, new_throat_count + Np]))
bound_vert_index.append(dict(zip(v, throat_verts)))
throat_vert_index.append(dict(zip(v, throat_verts)))
new_throat_count += 1
# Add new pores and connections
self.extend(pore_coords=bound_coords, throat_conns=bound_conns)
# Record new number of pores
Mp = self.num_pores()
Mt = self.num_throats()
new_pore_ids = np.arange(Np, Mp)
new_throat_ids = np.arange(Nt, Mt)
# Identify which boundary the pore sits on
front = self.pores()[self['pore.coords'][:, 0] == min_point[0]]
back = self.pores()[self['pore.coords'][:, 0] == max_point[0]]
left = self.pores()[self['pore.coords'][:, 1] == min_point[1]]
right = self.pores()[self['pore.coords'][:, 1] == max_point[1]]
bottom = self.pores()[self['pore.coords'][:, 2] == min_point[2]]
top = self.pores()[self['pore.coords'][:, 2] == max_point[2]]
if len(top) == 0:
top = self.pores()[self['pore.coords'][:, 2] == np.asarray(
bound_coords)[:, 2].max()]
# Assign labels
self['pore.boundary'] = False
self['pore.boundary'][new_pore_ids] = True
self['throat.boundary'] = False
self['throat.boundary'][new_throat_ids] = True
self['pore.right_boundary'] = False
self['pore.left_boundary'] = False
self['pore.front_boundary'] = False
self['pore.back_boundary'] = False
self['pore.top_boundary'] = False
self['pore.bottom_boundary'] = False
self['pore.right_boundary'][right] = True
self['pore.left_boundary'][left] = True
self['pore.front_boundary'][front] = True
self['pore.back_boundary'][back] = True
self['pore.top_boundary'][top] = True
self['pore.bottom_boundary'][bottom] = True
# Save the throat verts
self["pore.vert_index"][new_pore_ids] = bound_vert_index
self["throat.vert_index"][new_throat_ids] = throat_vert_index
def _calc_eff_prop(self, check_health=False):
r"""
This returns the main parameters for calculating the effective
property in a linear transport equation. It also checks for the
proper boundary conditions, inlets and outlets.
Parameters
----------
check_health : boolean (optional)
It analyzes the inlet and outlet pores to check their spatial
positions
"""
try:
self[self._quantity]
except KeyError:
raise Exception('The algorithm has not been run yet. Cannot ' +
'calculate effective property.')
# Determine boundary conditions by analyzing algorithm object
Ps = self.pores('pore.Dirichlet')
BCs = sp.unique(self['pore.bcval_Dirichlet'][Ps])
if sp.shape(BCs)[0] != 2:
raise Exception('The supplied algorithm did not have appropriate' +
' BCs')
inlets = sp.where(self['pore.' + 'bcval_Dirichlet'] == sp.amax(BCs))[0]
outlets = sp.where(self['pore.' +
'bcval_Dirichlet'] == sp.amin(BCs))[0]
# Analyze input and output pores
if check_health:
# Check for coplanarity
if self._net.iscoplanar(inlets) is False:
raise Exception('The inlet pores do not define a plane. ' +
'Effective property will be approximation')
if self._net.iscoplanar(outlets) is False:
raise Exception('The outlet pores do not define a plane. ' +
'Effective property will be approximation')
# Ensure pores are on a face of domain
# (only 1 non-self neighbor each)
PnI = self._net.find_neighbor_pores(pores=inlets,
mode='not_intersection',
excl_self=True)
if sp.shape(PnI) != sp.shape(inlets):
logger.warning('The inlet pores have too many neighbors. ' +
'Internal pores appear to be selected.')
pass
PnO = self._net.find_neighbor_pores(pores=outlets,
mode='not_intersection',
excl_self=True)
if sp.shape(PnO) != sp.shape(outlets):
logger.warning('The outlet pores have too many neighbors. ' +
'Internal pores appear to be selected.')
pass
# Fetch area and length of domain
if 'pore.vert_index' in self._net.props():
A = vo.vertex_dimension(network=self._net,
face1=inlets,
parm='area')
L = vo.vertex_dimension(network=self._net,
face1=inlets,
face2=outlets,
parm='length')
else:
A = self._net.domain_area(face=inlets)
L = self._net.domain_length(face_1=inlets, face_2=outlets)
flow = self.rate(pores=inlets)
D = sp.sum(flow) * L / A / (BCs[0] - BCs[1])
return D
def add_boundaries(self):
r"""
This method identifies pores in the original Voronoi object that straddle a boundary imposed by the reflection
The pore inside the original set of pores (with index 0 - Np) is identified and the coordinates are saved
The vertices making up the boundary throat are retrieved from the ridge_dict values and these are used to identify
which boundary the throat sits at.
A new pore and new connection is created with coordinates lying on the boundary plane
N.B This method will only work properly if the original network remains unaltered i.e. not trimmed or extended
This preserves the connection between pore index on the network object and the Voronoi object
The point of using this method is so that the throat vertices created by the Voronoi object are preserved
This method will create boundary pores at the centre of the voronoi faces that
align with the outer planes of the domain.
The original pores in the domain are labelled internal and the boundary pores
are labelled external
Examples
--------
>>> import OpenPNM
>>> pn = OpenPNM.Network.Delaunay(num_pores=100, domain_size=[0.0001,0.0001,0.0001])
>>> pn.add_boundaries()
>>> pn.num_pores("boundary")>0
True
"""
bound_conns=[]
bound_coords=[]
bound_vert_index=[]
throat_vert_index=[]
#Find boundary extent
[x_min,x_max,y_min,y_max,z_min,z_max]=vo.vertex_dimension(self,self.pores(),parm='minmax')
min_point = np.around(np.array([x_min,y_min,z_min]),10)
max_point = np.around(np.array([x_max,y_max,z_max]),10)
Np = self.num_pores()
Nt = self.num_throats()
new_throat_count = 0
# ridge_dict contains a dictionary where the key is a set of 2 neighbouring pores and the value is the vertex indices
# that form the throat or ridge between them
for p,v in self._vor.ridge_dict.items():
# if the vertex with index -1 is contained in list then the ridge is unbounded - ignore these
if np.all(np.asarray(v) >=0):
#boundary throats will be those connecting one pore inside the original set and one out
if (p[0] in range(Np) and p[1] not in range(Np)) or\
(p[0] not in range(Np) and p[1] in range(Np)):
# the dictionary key is not in numerical order so find the pore index inside
if p[0] in range(Np):
my_pore=p[0]
else:
my_pore=p[1]
my_pore_coord = self["pore.coords"][my_pore]
new_pore_coord = my_pore_coord.copy()
#rounding necessary here to identify the plane as Voronoi can have 1e-17 and smaller errors
throat_verts = np.around(self._vor.vertices[v],10)
#find which plane we are aligned with (if any) and align new_pore with throat plane
if len(np.unique(throat_verts[:,0])) == 1:
new_pore_coord[0]=np.unique(throat_verts[:,0])
elif len(np.unique(throat_verts[:,1])) == 1:
new_pore_coord[1]=np.unique(throat_verts[:,1])
elif len(np.unique(throat_verts[:,2])) == 1:
new_pore_coord[2]=np.unique(throat_verts[:,2])
else:
new_pore_coord = throat_verts.mean()
bound_coords.append(new_pore_coord)
bound_conns.append(np.array([my_pore,new_throat_count+Np]))
bound_vert_index.append(dict(zip(v,throat_verts)))
throat_vert_index.append(dict(zip(v,throat_verts)))
new_throat_count += 1
#Add new pores and connections
self.extend(pore_coords=bound_coords, throat_conns=bound_conns)
#Record new number of pores
Mp = self.num_pores()
Mt = self.num_throats()
new_pore_ids = np.arange(Np,Mp)
new_throat_ids = np.arange(Nt,Mt)
#Identify which boundary the pore sits on
front = self.pores()[self['pore.coords'][:,0]==min_point[0]]
back = self.pores()[self['pore.coords'][:,0]==max_point[0]]
left = self.pores()[self['pore.coords'][:,1]==min_point[1]]
right = self.pores()[self['pore.coords'][:,1]==max_point[1]]
bottom = self.pores()[self['pore.coords'][:,2]==min_point[2]]
top = self.pores()[self['pore.coords'][:,2]==max_point[2]]
#Assign labels
self['pore.boundary'] = False
self['pore.boundary'][new_pore_ids] = True
self['pore.right_boundary'] = False
self['pore.left_boundary'] = False
self['pore.front_boundary'] = False
self['pore.back_boundary'] = False
self['pore.top_boundary'] = False
self['pore.bottom_boundary'] = False
self['pore.right_boundary'][right] = True
self['pore.left_boundary'][left] = True
self['pore.front_boundary'][front] = True
self['pore.back_boundary'][back] = True
self['pore.top_boundary'][top] = True
self['pore.bottom_boundary'][bottom] = True
#Save the throat verts
self["pore.vert_index"][new_pore_ids] = bound_vert_index
self["throat.vert_index"][new_throat_ids] = throat_vert_index