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 setup3D(mesh=None, **params):
# pass mesh argument to prevent mesh regeneration
global x0
global geo3D # to prevent garbage collection of mesh
globals().update(params)
if x0 is not None:
x0 = [round(t, 4) for t in x0]
geop = geo_params3D(x0, rMolecule, Rx, Ry, lcpore)
physp = phys_params(bV, Qmol, dnaqsdamp, rMolecule, bulkcon)
if mesh is None:
generate_mesh(h3D, geo_name3D, **geop)
geo = geo_from_name(geo_name3D, **geop)
else:
geo = geo_from_name(geo_name3D, mesh=mesh, **geop)
# define cylinders for inner and outer DNA boundary and side boundary
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"])
# this causes geo to automatically snap boundaries when adapting
geo.curved = dict(
innerdnab=innerdna.snap,
outerdnab=outerdna.snap,
membranednab=outerdna.snap,
sideb=side.snap,
outermembraneb=side.snap,
)
# define sphere for molecule
if x0 is not None:
molec = Sphere(R=geo.params["rMolecule"], center=geo.params["x0"])
geo.curved.update(moleculeb=molec.snap)
phys = Physics(phys_name, geo, **physp)
#phys.permittivity = {"default": phys.permittivity["water"]}
return geo, phys
w0 = w3D(u=u, p=p)
# 1D visualization
#Rz = geo2D.params["Rz"]
#r0 = geo2D.params["r0"]
#plot1D({"phi (2D)": pb2D.solution}, (-Rz, Rz, 101), "y", dim=2, origin=(r0, 0.))
#plot1D({"phi (2D)": pb2D.solution}, (-Rz, Rz, 101), "y", dim=2, origin=(0., 0.))
# 3D geometry
meshgen_dict = generate_mesh(h, geo_name, **geo_params)
geo = geo_from_name(geo_name, **geo_params)
# define sphere for molecule
molec = Sphere(R=geo.params["rMolecule"], center=geo.params["x0"])
# define cylinders for inner and outer DNA boundary and side boundary
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"])
# this causes geo to automatically snap boundaries when adapting
geo.curved = dict(
moleculeb=molec.snap,
innerdnab=innerdna.snap,
outerdnab=outerdna.snap,
membranednab=outerdna.snap,
sideb=side.snap,
outermembraneb=side.snap,
)
phys = Physics("howorka", geo, **phys_params)
IllposedLinearSolver.stab = 1e9
bulk = {"upperb", "lowerb"},
#nocbc = {"lowerb"},
)
geo2D = domain2D.create_geometry(lc=h2D)
print "Number of cells (2D):", geo2D.mesh.num_cells()
#domain2D.plot()
# --- create 3D geometry by rotating ---
domain3D = rotate_z(domain2D)
geo3D = domain3D.create_geometry(lc=h3D)
print "Number of cells (3D):", geo3D.mesh.num_cells()
#domain3D.plot()
# define cylinder
cyl = Cylinder(R=R, L=2.*Rz)
# this causes geo to automatically snap boundaries when adapting
geo3D.curved = dict(wall = cyl.snap)
# --- create geometry for 1D crossection ---
# TODO: it would be cool if the 1D domain could be extracted from the 2D one
# (should be pretty easy)
domain1D = Interval(0., R)
domain1D.addsubdomain(domain1D, "fluid")
domain1D.addboundaries(
wall = domain1D.boundary("right"),
center = domain1D.boundary("left")
)
domain1D.params["lscale"] = 1e9
domain1D.synonymes = dict(
pore = "fluid",