def test_pickle_csg():
import netgen.csg as csg
geo = csg.CSGeometry()
geo.Add(csg.Sphere(csg.Pnt(0,0,0), 2).bc("sphere"))
brick = csg.OrthoBrick(csg.Pnt(-3,-3,-3), csg.Pnt(3,3,3))
geo.Add(csg.Cylinder(csg.Pnt(0,0,0), csg.Pnt(1,0,0), 0.5) * brick)
geo.Add(csg.Ellipsoid(csg.Pnt(0,0,0), csg.Vec(1,0,0), csg.Vec(0,1,0), csg.Vec(0,0,0.5)))
geo.Add(csg.Cone(csg.Pnt(0,0,0), csg.Pnt(3,0,0), 1, 0.5) * brick)
geo.Add(csg.EllipticCone(csg.Pnt(0,0,0), csg.Vec(2,0,0), csg.Vec(0,1,0), 3, 0.5) * brick)
geo.Add(csg.Torus(csg.Pnt(0,0,0), csg.Vec(0,1,0), 0.3, 0.05))
pts2d = [[1,1], [1,-1], [-1,-1], [-1,1]]
segs = [[0,1], [1,2], [2,3], [3,0]]
curve = csg.SplineCurve2d()
pnrs = [curve.AddPoint(*p) for p in pts2d]
for s in segs:
curve.AddSegment(pnrs[s[0]], pnrs[s[1]])
geo.Add(csg.Revolution(csg.Pnt(0,0,0), csg.Pnt(1,0,0), curve))
path = csg.SplineCurve3d()
pnts = [(0,0,0), (2,0,0), (2,2,0)]
segs = [(0,1,2)]
for pnt in pnts:
path.AddPoint (*pnt)
for seg in segs:
path.AddSegment (*seg)
geo.Add(csg.Extrusion(path, curve, csg.Vec(0,0,1)))
geo_dump = pickle.dumps(geo)
geo2 = pickle.loads(geo_dump)
vd1 = geo._visualizationData()
vd2 = geo2._visualizationData()
for val1, val2 in zip(vd1.values(), vd2.values()):
assert numpy.array_equal(val1, val2)
def __init__(self, pointa, pointb, radius, *, eps=csg_eps):
unit = 1. * numpy.array(pointb) - numpy.array(pointa)
unit /= numpy.linalg.norm(unit)
eps *= radius
super().__init__(
netgen_csg.Cylinder(netgen_csg.Pnt(*pointa),
netgen_csg.Pnt(*pointb), radius),
csg_boundaries=[
dolfin.CompiledSubDomain(
'on_boundary && near((x[0]-p0)*(x[0]-p0) + (x[1]-p1)*(x[1]-p1) + (x[2]-p2)*(x[2]-p2) - ((x[0]-p0)*u0 + (x[1]-p1)*u1 + (x[2]-p2)*u2)*((x[0]-p0)*u0 + (x[1]-p1)*u1 + (x[2]-p2)*u2), rr, eps)',
u0=unit[0],
u1=unit[1],
u2=unit[2],
p0=pointa[0],
p1=pointa[1],
p2=pointa[2],
rr=radius * radius,
eps=eps)
])
def save(cls,
network,
phases=[],
filename='',
maxsize='auto',
fileformat='STL Format',
logger_level=0):
r"""
Saves (transient/steady-state) data from the given objects into the
specified file.
Parameters
----------
network : OpenPNM Network Object.
The network containing the desired data.
phases : list of OpenPNM Phase Objects (place holder, default is none).
filename : string (optional).
The name of the file containing the data to export.
maxsize : a float or a string "auto" (optional).
The maximum size of the mesh elements allowed. "auto" corresponds
to an automatic determination based on pores and throats sizes. Any
float value will be used as a maximum size. Small values result in
finner meshes, but slower mesh calculations.
fileformat : string (optional).
Default is "STL Format" which corresponds to STL format. Other
formats such as Gmsh and Fluent are supported (see ngsolve.org).
logger_level : integer between 0 and 7 (optional).
Default is 0. The logger level set in netgen package.
Notes
-----
This method only saves the geometry of the network, not any of the
pore-scale models or other attributes. To save an actual OpenPNM
Project use the ``Workspace`` object.
"""
try:
import netgen.csg as csg
except ModuleNotFoundError:
logger.error('Module "netgen.csg" not found.')
try:
from netgen.meshing import SetMessageImportance as log
log(logger_level)
except ModuleNotFoundError:
logger.warning('Module "netgen.meshing" not found. ' +
'The "logger_level" ignored.')
project, network, phases = cls._parse_args(network=network,
phases=phases)
network = network[0]
if filename == '':
filename = project.name
path = cls._parse_filename(filename=filename, ext='stl')
# Path is a pathlib object, so slice it up as needed
fname_stl = path.name
# correct connections where 'pore.diameter' = 'throat.diameter'
dt = network['throat.diameter'].copy()
dp = network['pore.diameter'][network['throat.conns']]
dt[dp[:, 0] == dt] *= 0.99
dt[dp[:, 1] == dt] *= 0.99
scale = max(network['pore.diameter'].max(), dt.max(),
network['throat.length'].max())
if maxsize == 'auto':
maxsize = min(network['pore.diameter'].min(), dt.min(),
network['throat.length'].min())
geo = csg.CSGeometry()
# define pores
geometry = csg.Sphere(
csg.Pnt(network['pore.coords'][0, 0] / scale,
network['pore.coords'][0, 1] / scale,
network['pore.coords'][0, 2] / scale),
network['pore.diameter'][0] / scale / 2)
for p in range(1, network.Np):
pore = csg.Sphere(
csg.Pnt(network['pore.coords'][p, 0] / scale,
network['pore.coords'][p, 1] / scale,
network['pore.coords'][p, 2] / scale),
network['pore.diameter'][p] / scale / 2)
geometry += pore
# define throats
for t in range(network.Nt):
A = network['throat.endpoints.tail'][t, :] / scale
B = network['throat.endpoints.head'][t, :] / scale
V = (B - A) / _np.linalg.norm(B - A)
plane1 = csg.Plane(csg.Pnt(A[0], A[1], A[2]),
csg.Vec(-V[0], -V[1], -V[2]))
plane2 = csg.Plane(csg.Pnt(B[0], B[1], B[2]),
csg.Vec(V[0], V[1], V[2]))
cylinder = csg.Cylinder(csg.Pnt(A[0], A[1], A[2]),
csg.Pnt(B[0], B[1], B[2]),
dt[t] / scale / 2)
throat = cylinder * plane1 * plane2
geometry += throat
# add pore and throats to geometry, build mesh, rescale, and export
geo.Add(geometry)
mesh = geo.GenerateMesh(maxh=maxsize / scale)
mesh.Scale(scale)
mesh.Export(filename=fname_stl, format=fileformat)