def test_SurfaceGetFE(quads=False):
# 2d surface in 3d tests
import netgen.meshing as meshing
import netgen.csg as csg
geo = csg.CSGeometry()
bottom = csg.Plane(csg.Pnt(0, 0, 0), csg.Vec(0, 0, 1))
surface = csg.SplineSurface(bottom)
pts = [(0, 0, 0), (0, 1, 0), (1, 1, 0), (1, 0, 0)]
geopts = [surface.AddPoint(*p) for p in pts]
for p1, p2, bc in [(0, 1, "left"), (1, 2, "top"), (2, 3, "right"),
(3, 0, "bottom")]:
surface.AddSegment(geopts[p1], geopts[p2], bc)
geo.AddSplineSurface(surface)
mesh = Mesh(
geo.GenerateMesh(perfstepsend=meshing.MeshingStep.MESHSURFACE,
quad=quads))
for spacename in surfacespaces.keys():
if quads and spaces2d[spacename]["quad"]:
for order in surfacespaces[spacename]["order"]:
space = FESpace(type=spacename, mesh=mesh, order=order)
for vb in surfacespaces[spacename]["vorb"]:
for el in space.Elements(vb):
assert space.GetFE(el).ndof == len(
space.GetDofNrs(el)), [spacename, vb, order]
return
def test_pickle_surface_fespaces():
import netgen.meshing as meshing
import netgen.csg as csg
geo = csg.CSGeometry()
bottom = csg.Plane(csg.Pnt(0, 0, 0), csg.Vec(0, 0, 1))
surface = csg.SplineSurface(bottom)
pts = [(0, 0, 0), (0, 1, 0), (1, 1, 0), (1, 0, 0)]
geopts = [surface.AddPoint(*p) for p in pts]
for p1, p2, bc in [(0, 1, "left"), (1, 2, "top"), (2, 3, "right"),
(3, 0, "bottom")]:
surface.AddSegment(geopts[p1], geopts[p2], bc)
geo.AddSplineSurface(surface)
mesh = Mesh(
geo.GenerateMesh(maxh=0.3,
perfstepsend=meshing.MeshingStep.MESHSURFACE))
spaces = [
HDivDivSurface(mesh, order=3, dirichlet=[1, 2, 3, 4]),
FacetSurface(mesh, order=3, dirichlet=[1, 2, 3, 4]),
HDivSurface(mesh, order=3, dirichlet=[1, 2, 3, 4])
]
for space in spaces:
with io.BytesIO() as f:
pickler = pickle.Pickler(f)
pickler.dump(space)
data = f.getvalue()
with io.BytesIO(data) as f:
unpickler = pickle.Unpickler(f)
space2 = unpickler.load()
assert space.ndof == space2.ndof
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 gen_3dbeam(maxh, nref, comm, lens=[10, 1, 1]):
b = csg.OrthoBrick(csg.Pnt(-1, 0, 0), csg.Pnt(lens[0], lens[1],
lens[2])).bc("other")
p = csg.Plane(csg.Pnt(0, 0, 0), csg.Vec(-1, 0, 0)).bc("left")
geo = csg.CSGeometry()
geo.Add(b * p)
return gen_ref_mesh(geo, maxh, nref, comm)
def test_pickle_mesh():
import netgen.csg as csg
geo1 = csg.CSGeometry()
geo2 = csg.CSGeometry()
brick = csg.OrthoBrick(csg.Pnt(-3, -3, -3), csg.Pnt(3, 3, 3))
geo2.Add(brick)
for geo in [geo1, geo2]:
mesh = geo.GenerateMesh(maxh=2)
assert geo == mesh.GetGeometry()
dump = pickle.dumps([geo, mesh])
geo2, mesh2 = pickle.loads(dump)
assert geo2 == mesh2.GetGeometry()
mesh.Save("msh1.vol.gz")
mesh2.Save("msh2.vol.gz")
import filecmp, os
assert filecmp.cmp("msh1.vol.gz", "msh2.vol.gz")
os.remove("msh1.vol.gz")
os.remove("msh2.vol.gz")
def generateMesh(filename, mp):
folder = os.path.join("..", "..",
"tutorials") if filename in _geofiles else "geofiles"
if filename.endswith(".geo"):
geo = csg.CSGeometry(os.path.join(folder, filename))
elif filename.endswith(".stl"):
geo = stl.STLGeometry(os.path.join(folder, filename))
elif filename.endswith(".step"):
geo = occ.OCCGeometry(os.path.join(folder, filename))
return geo.GenerateMesh(mp)
def cube_geo():
origin = csg.Pnt(0, 0, 0)
side = 1
box = csg.OrthoBrick(origin, csg.Pnt(side, 2 * side,
side)).bc('cube_outer')
normal_vec = csg.Vec(0, 1, 0)
topplane = csg.Plane(csg.Pnt(0, 1, 0), normal_vec).bc('dirichlet')
cube = (box * topplane).mat('cube_mat')
cube_geom = csg.CSGeometry()
cube_geom.Add(cube)
return cube_geom
def hinges_3d(N=4, touch=True):
geo = csg.CSGeometry()
plane_left = csg.Plane(csg.Pnt(0, 0, 0), csg.Vec(-1, 0, 0)).bc("left")
plane_right = csg.Plane(csg.Pnt(1, 0, 0), csg.Vec(1, 0, 0)).bc("outer")
plane_bot = csg.Plane(csg.Pnt(0, 0, 0), csg.Vec(0, -1, 0)).bc("outer")
plane_top = csg.Plane(csg.Pnt(0, 1, 0), csg.Vec(0, 1, 0)).bc("outer")
plane_back = csg.Plane(csg.Pnt(0, 0, 0), csg.Vec(0, 0, -1)).bc("outer")
plane_front = csg.Plane(csg.Pnt(0, 0, 1), csg.Vec(0, 0, 1)).bc("outer")
box = csg.OrthoBrick(csg.Pnt(-0.1, -0.1, -0.1),
csg.Pnt(1, 1, 1)).mat("mat_a").bc("outer")
# N hinges, so N+1 boxes, or N+2 if we do not want to touch diri
h = 1 / (N + 1)
hinges = list()
if touch:
h0 = csg.OrthoBrick(csg.Pnt(-0.1, -0.1, -0.1),
csg.Pnt(h, h, 1.1)).mat("mat_b").bc("inner")
hinges.append(h0)
rmin = 1
rmax = N
hinges = hinges + [
csg.OrthoBrick(csg.Pnt(k * h, k * h, -0.1),
csg.Pnt((k + 1) * h,
(k + 1) * h, 1.1)).mat("mat_b").bc("inner")
for k in range(rmin, rmax)
]
hl = csg.OrthoBrick(csg.Pnt(N * h, N * h, -0.1),
csg.Pnt(1.1, 1.1, 1.1)).mat("mat_b").bc("inner")
hinges.append(hl)
bmh = box - hinges[0]
hs = hinges[0]
for h in hinges[1:]:
hs = hs + h
bmh = bmh - h
geo.Add(bmh * plane_left * plane_right * plane_bot * plane_top *
plane_back * plane_front)
geo.Add(hs * plane_left * plane_right * plane_bot * plane_top *
plane_back * plane_front)
return geo
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)
def _loadGeo(gui, filename):
import netgen.csg as csg
geo = csg.CSGeometry(filename)
ngsolve.Draw(geo)
def __init__(self):
self.collection = netgen_csg.CSGeometry()
self.csg_boundaries = []
def get_Netgen_nonconformal(N, scale, offset, dim=2):
"""
Generate a structured quadrilateral/hexahedral NGSolve mesh over a
prescribed square/cubic domain.
Args:
N (list): Number of mesh elements in each direction (N+1 nodes).
scale (list): Extent of the meshed domain in each direction ([-2,2]
square -> scale=[4,4]).
offset (list): Centers the meshed domain in each direction ([-2,2]
square -> offset=[2,2]).
dim (int): Dimension of the domain (must be 2 or 3).
Returns:
mesh (Netgen mesh): Structured quadrilateral/hexahedral Netgen mesh.
"""
# Construct a Netgen mesh.
ngmesh = ngmsh.Mesh()
if dim == 2:
ngmesh.SetGeometry(unit_square)
ngmesh.dim = 2
# Set evenly spaced mesh nodes.
points = []
for i in range(N[1] + 1):
for j in range(N[0] + 1):
x = -offset[0] + scale[0] * j / N[0]
y = -offset[1] + scale[1] * i / N[1]
z = 0
points.append(ngmesh.Add(ngmsh.MeshPoint(ngmsh.Pnt(x, y, z))))
# TODO: Should the user be able to set their own BC names?
idx_dom = ngmesh.AddRegion('dom', dim=2)
idx_bottom = ngmesh.AddRegion('bottom', dim=1)
idx_right = ngmesh.AddRegion('right', dim=1)
idx_top = ngmesh.AddRegion('top', dim=1)
idx_left = ngmesh.AddRegion('left', dim=1)
# Generate mesh faces.
for i in range(N[1]):
for j in range(N[0]):
p1 = i * (N[0] + 1) + j
p2 = i * (N[0] + 1) + j + 1
p3 = i * (N[0] + 1) + j + 2 + N[0]
p4 = i * (N[0] + 1) + j + 1 + N[0]
ngmesh.Add(ngmsh.Element2D(idx_dom, [points[p1], points[p2], points[p3], points[p4]]))
# Assign each edge of the domain to the same boundary.
for i in range(N[1]):
ngmesh.Add(ngmsh.Element1D([points[N[0] + i * (N[0] + 1)], points[N[0] + (i + 1) * (N[0] + 1)]], index=idx_right))
ngmesh.Add(ngmsh.Element1D([points[(i + 1) * (N[0] + 1)], points[i * (N[0] + 1)]], index=idx_left))
for i in range(N[0]):
ngmesh.Add(ngmsh.Element1D([points[i], points[i + 1]], index=idx_bottom))
ngmesh.Add(ngmsh.Element1D([points[1 + i + N[1] * (N[0] + 1)], points[i + N[1] * (N[0] + 1)]], index=idx_top))
elif dim == 3:
ngmesh.dim = 3
p1 = (0, 0, 0)
p2 = (1, 1, 1)
cube = ngcsg.OrthoBrick(ngcsg.Pnt(p1[0], p1[1], p1[2]), ngcsg.Pnt(p2[0], p2[1], p2[2])).bc(1)
geo = ngcsg.CSGeometry()
geo.Add(cube)
ngmesh.SetGeometry(geo)
# Set evenly spaced mesh nodes.
points = []
for i in range(N[0] + 1):
for j in range(N[1] + 1):
for k in range(N[2] + 1):
x = -offset[0] + scale[0] * i / N[0]
y = -offset[1] + scale[1] * j / N[1]
z = -offset[2] + scale[2] * k / N[2]
points.append(ngmesh.Add(ngmsh.MeshPoint(ngmsh.Pnt(x, y, z))))
# Generate mesh cells.
for i in range(N[0]):
for j in range(N[1]):
for k in range(N[2]):
base = i * (N[1] + 1) * (N[2] + 1) + j * (N[2] + 1) + k
baseup = base + (N[1] + 1) * (N[2] + 1)
p1 = base
p2 = base + 1
p3 = base + (N[2] + 1) + 1
p4 = base + (N[2] + 1)
p5 = baseup
p6 = baseup + 1
p7 = baseup + (N[2] + 1) + 1
p8 = baseup + (N[2] + 1)
idx = 1
ngmesh.Add(ngmsh.Element3D(idx,
[points[p1], points[p2], points[p3], points[p4], points[p5], points[p6],
points[p7], points[p8]]))
def add_bc(p, d, N, deta, neta, facenr):
def add_seg(i, j, os):
base = p + i * d + j * deta
p1 = base
p2 = base + os
ngmesh.Add(ngmsh.Element1D([points[p1], points[p2]], index=facenr))
return
for i in range(N):
for j in [0, neta]:
add_seg(i, j, d)
for i in [0, N]:
for j in range(neta):
add_seg(i, j, deta)
for i in range(N):
for j in range(neta):
base = p + i * d + j * deta
p1 = base
p2 = base + d
p3 = base + d + deta
p4 = base + deta
ngmesh.Add(ngmsh.Element2D(facenr, [points[p1], points[p2], points[p3], points[p4]]))
return
# Order is important!
ngmesh.Add(ngmsh.FaceDescriptor(surfnr=4, domin=1, bc=1))
ngmesh.Add(ngmsh.FaceDescriptor(surfnr=2, domin=1, bc=2))
ngmesh.Add(ngmsh.FaceDescriptor(surfnr=5, domin=1, bc=3))
ngmesh.Add(ngmsh.FaceDescriptor(surfnr=3, domin=1, bc=4))
ngmesh.Add(ngmsh.FaceDescriptor(surfnr=0, domin=1, bc=5))
ngmesh.Add(ngmsh.FaceDescriptor(surfnr=1, domin=1, bc=6))
# Assign each exterior face of the domain to its respective boundary.
add_bc(0, 1, N[2], N[2] + 1, N[1], 1)
add_bc(0, (N[1] + 1) * (N[2] + 1), N[0], 1, N[2], 2)
add_bc((N[0] + 1) * (N[1] + 1) * (N[2] + 1) - 1, -(N[2] + 1), N[1], -1, N[2], 3)
add_bc((N[0] + 1) * (N[1] + 1) * (N[2] + 1) - 1, -1, N[2], -(N[1] + 1) * (N[2] + 1), N[0], 4)
add_bc(0, N[2] + 1, N[1], (N[1] + 1) * (N[2] + 1), N[0], 5)
add_bc((N[0] + 1) * (N[1] + 1) * (N[2] + 1) - 1, -(N[1] + 1) * (N[2] + 1), N[0], -(N[2] + 1), N[1], 6)
# TODO: Should the user be able to specify their own bc names?
bc_names = {0: 'back', 1: 'left', 2: 'front', 3: 'right', 4: 'bottom', 5: 'top'}
for key, val in bc_names.items():
ngmesh.SetBCName(key, val)
else:
raise ValueError('Only works with 2D or 3D meshes.')
return ngmesh
