def init_geo(self):
if self.geop.dim == 3:
generate_mesh(self.solverp.h, geo_name3D, **self.geop)
geo = geo_from_name(geo_name3D, **self.geop)
# define cylinders for DNA and side boundaries
innerdna = Cylinder(R=geo.params["r0"], L=geo.params["l0"])
outerdna = Cylinder(R=geo.params["r1"], L=geo.params["l0"])
side = Cylinder(R=geo.params["R"], L=2. * geo.params["Rz"])
geo.curved = dict(
innerdnab=innerdna.snap,
outerdnab=outerdna.snap,
membranednab=outerdna.snap,
sideb=side.snap,
outermembraneb=side.snap,
)
# define sphere for molecule
if self.geop.x0 is not None:
molec = Sphere(R=geo.params["rMolecule"],
center=geo.params["x0"])
geo.curved.update(moleculeb=molec.snap)
if self.geop.dim == 2:
generate_mesh(self.solverp.h, geo_name, **self.geop)
geo = geo_from_name(geo_name, **self.geop)
#dolfin.plot(geo.boundaries)
#dolfin.interactive()
if self.geop.x0 is not None:
molec = Circle(geo.params["rMolecule"], geo.params["x0"][::2])
geo.curved = dict(moleculeb=molec.snap)
# compatibility with new style physics current
geo.params["lpore"] = geo.params["l0"]
self.geo = geo
def setup2D(**params):
global z0
globals().update(params)
if z0 is not None:
z0 = round(z0, 4)
geop = geo_params(z0)
physp = phys_params(bV, Qmol, dnaqsdamp)
generate_mesh(h, geo_name, **geop)
geo = geo_from_name(geo_name, **geop)
if z0 is not None:
molec = Circle(R=geo.params["rMolecule"], center=geo.params["x0"][::2])
geo.curved = dict(moleculeb=molec.snap)
phys = Physics(phys_name, geo, **physp)
#phys.permittivity = {"default": phys.permittivity["water"]}
return geo, phys
def setup2D(mesh=None, **params):
# pass mesh argument to prevent mesh regeneration
global z0
global geo # to prevent garbage collection of mesh
globals().update(params)
if z0 is not None:
z0 = round(z0, 4)
geop = geo_params(z0, rMolecule, Rx, Ry)
physp = phys_params(bV, Qmol, dnaqsdamp, rMolecule, bulkcon)
if mesh is None:
generate_mesh(h, geo_name, **geop)
geo = geo_from_name(geo_name, **geop)
else:
geo = geo_from_name(geo_name, mesh=mesh, **geop)
if z0 is not None:
molec = Circle(R=geo.params["rMolecule"], center=geo.params["x0"][::2])
geo.curved = dict(moleculeb=molec.snap)
phys = Physics(phys_name, geo, **physp)
#phys.permittivity = {"default": phys.permittivity["water"]}
return geo, phys
Qmol=-1. * qq,
bulkcon=3e2,
dnaqsdamp=1.,
bV=bV,
exactMqv=not adaptq,
adaptMqv=adaptq,
)
set_log_level(100)
Felref = 1.1424041805
Fdragref = -7.69122891958
# 2D geometry
generate_mesh(h2D, "H_geo", **geo_params2D)
geo2D = geo_from_name("H_geo", **geo_params)
molec2D = Circle(R=geo2D.params["rMolecule"], center=geo2D.params["x0"][::2])
geo2D.curved = dict(moleculeb=molec2D.snap)
mesh2D = geo2D.mesh
phys2D = Physics("howorka", geo2D, **phys_params)
IllposedLinearSolver.stab = 1e0
IllposedNonlinearSolver.newtondamp = 1.
PNPSAxisym.tolnewton = 1e-4
# solve 2D
print "\n---- SOLVE 2D PROBLEM ----"
pb2D, pnps2D = adaptive_pbpnps(geo2D,
phys2D,
cyl=True,
frac=frac,
from nanopores.geometries.curved import Cylinder, Circle, Boundary, snap_to_boundary
# Define rectangular domain
h = .4
domain = Box([0., 0.], [1., 1.])
domain.addsubdomains(main=domain)
domain.addboundaries(boundary=domain.boundary(), )
geo = domain.create_geometry(lc=h)
#boundaries = geo.boundaries
mesh = geo.mesh
# introduce circle
circ = Circle(R=.4, center=(.5, .5), frac=0.9)
subdomains = MeshFunction("size_t", mesh, mesh.topology().dim())
subdomains.set_all(0)
circ.mark(subdomains, 1)
plot(subdomains)
submesh = SubMesh(mesh, subdomains, 0)
#plot(mesh, title="initial")
plot(submesh, title="initial")
#plot(boundaries, title="initial")
submesh.snap_boundary(circ, True)
#plot(mesh, title="after snapping")
#plot(submesh, title="after snapping")
# mark circle boundary in geo.boundaries