import logging
import numpy as np
from openpnm.network import Network
from openpnm.utils import Docorator
from openpnm import topotools
from openpnm import _skgraph as skgr
skgr.settings.node_prefix = 'pore'
skgr.settings.edge_prefix = 'throat'
docstr = Docorator()
logger = logging.getLogger(__name__)
__all__ = ['Cubic']
[docs]
@docstr.dedent
class Cubic(Network):
r"""
Simple cubic lattice with connectivity from 6 to 26
Though simple, the Cubic network offers many advantages such as easy
visualization and accurate determination of domain area and length in
transport calculations.
Parameters
----------
shape : array_like
The [Nx, Ny, Nz] size of the network in terms of the number of pores
in each direction. For a 2D network
spacing : array_like, optional
The spacing between pore centers in each direction. If not given,
then [1, 1, 1] is assumed.
connectivity : int, optional
The number of connections to neighboring pores. Connections are made
symmetrically to any combination of face, edge, or corners neighbors.
The default is 6 to create a simple cubic structure, but options are:
=========== =====================================================
Value Result
=========== =====================================================
6 Faces only
14 Faces and Corners
18 Faces and Edges
20 Edges and Corners
26 Faces, Edges and Corners
=========== =====================================================
For a more random distribution of connectivity, use a high
``connectivity`` (i.e. 26) and then delete a fraction of the throats
using ``openpnm.topotools.reduce_coordination``. Also note that
corners-only and edges-only are not permitted since they create
disconnected networks. If you require one of these topologies you
can specify 14 or 18, then use ``openpnm.topotools.trim`` to remove
the face-to-face connections, which can be identified by looking
for throats with a length equal to the network spacing.
%(Network.parameters)s
"""
def __init__(self, shape, spacing=[1, 1, 1], connectivity=6, **kwargs):
super().__init__(**kwargs)
net = skgr.generators.cubic(shape=shape, spacing=spacing,
connectivity=connectivity,
node_prefix='pore', edge_prefix='throat')
self.update(net)
self._post_init()
self["pore.surface"] = skgr.tools.find_surface_nodes_cubic(self)
Ps = self["pore.surface"]
self["throat.surface"] = np.all(Ps[self["throat.conns"]], axis=1)
self.update(skgr.generators.tools.label_faces_cubic(self))
[docs]
def add_boundary_pores(self, labels=["top", "bottom", "front",
"back", "left", "right"],
spacing=None):
r"""
Add pores to the faces of the network for use as boundary pores.
Pores are offset from the faces by 1/2 a lattice spacing such that
they lie directly on the boundaries.
Parameters
----------
labels : str or list[str]
The labels indicating the pores defining each face where
boundary pores are to be added (e.g. 'left' or
['left', 'right'])
spacing : scalar or array_like
The spacing of the network (e.g. [1, 1, 1]). This should be
given since it can be quite difficult to infer from the
network, for instance if boundary pores have already added to
other faces.
"""
if isinstance(labels, str):
labels = [labels]
x, y, z = self["pore.coords"].T
if spacing is None:
spacing = skgr.tools.get_cubic_spacing(self)
else:
spacing = np.array(spacing)
if spacing.size == 1:
spacing = np.ones(3) * spacing
Lcx, Lcy, Lcz = spacing
offset = {}
shape = skgr.tools.get_cubic_shape(self)
offset["front"] = offset["left"] = offset["bottom"] = [0, 0, 0]
offset["right"] = [Lcx * shape[0], 0, 0]
offset["back"] = [0, Lcy * shape[1], 0]
offset["top"] = [0, 0, Lcz * shape[2]]
scale = {}
scale["left"] = scale["right"] = [0, 1, 1]
scale["front"] = scale["back"] = [1, 0, 1]
scale["bottom"] = scale["top"] = [1, 1, 0]
for label in labels:
try:
Ps = self.pores(label)
topotools.clone_pores(network=self, pores=Ps,
labels=f"{label}_boundary",
mode='parents')
# Translate cloned pores
ind = self.pores(label + "_boundary")
coords = self["pore.coords"][ind]
coords = coords * scale[label] + offset[label]
self["pore.coords"][ind] = coords
except KeyError:
msg = f"No pores labelled {label} found, skipping boundary addition"
logger.warning(msg)
