def build(self):
params = self.params
h = self.h
if params.diamPore is not None:
diamPore = params.diamPore # inner (effective) pore diameter
diamDNA = params.diamDNA # dna diameter of outer dna layers
l0 = diamPore + 6. * diamDNA
l1 = diamPore + 4. * diamDNA
l2 = diamPore + 2. * diamDNA
l3 = diamPore
l4 = l1
params.update(l0=l0, l1=l1, l2=l2, l3=l3, l4=l4)
if params.dim == 3:
geo = pughpore.get_geo(h, **params)
if geo.params["x0"] is not None:
molec = curved.Sphere(geo.params["rMolecule"],
geo.params["x0"])
geo.curved = dict(moleculeb=molec.snap)
elif params.dim == 2:
geo = pughpore.get_geo_cyl(h, **params)
if geo.params["x0"] is not None:
molec = curved.Circle(geo.params["rMolecule"],
geo.params["x0"])
geo.curved = dict(moleculeb=molec.snap)
elif params.dim == 1:
geo = pughpore.get_geo1D(h, **params)
return geo
def init_geo(self, create_geo=True):
if self.geop.diamPore is not None:
diamPore = self.geop.diamPore # inner (effective) pore diameter
diamDNA = self.geop.diamDNA # dna diameter of outer dna layers
l0 = diamPore + 6.*diamDNA
l1 = diamPore + 4.*diamDNA
l2 = diamPore + 2.*diamDNA
l3 = diamPore
l4 = l1
self.geop.update(l0=l0, l1=l1, l2=l2, l3=l3, l4=l4)
if not create_geo:
self.geo = None
return
if self.geop.dim == 3:
geo = pughpore.get_geo(self.solverp.h, **self.geop)
if geo.params["x0"] is not None:
molec = nano.curved.Sphere(geo.params["rMolecule"],
geo.params["x0"])
geo.curved = dict(moleculeb = molec.snap)
if self.geop.dim == 2:
geo = pughpore.get_geo_cyl(self.solverp.h, **self.geop)
if geo.params["x0"] is not None:
molec = nano.curved.Circle(geo.params["rMolecule"],
geo.params["x0"][::2])
geo.curved = dict(moleculeb = molec.snap)
self.geo = geo
def distance_boundary():
h = up.h
geo = pughpore.get_geo(h)
y = distance_boundary_from_geo(geo)
print "Max distance:", y.vector().max()
if not fields.exists("pugh_distance", h=h):
fields.save_functions("pugh_distance", dict(h=h), y=y)
fields.update()
return y
bulkcon=300.,
dnaqsdamp=.5,
bV=-0.1,
)
solverp = nano.Params(
h=up.h,
frac=0.2,
Nmax=up.Nmax,
imax=30,
tol=1e-2,
cheapest=False,
)
# setup geometry and physics
box.set_tol(None)
geo = pughpore.get_geo(solverp.h, **geop)
#print geo
#nano.plot_sliced(geo)
#dolfin.interactive()
molec = Sphere(R=geo.params["rMolecule"], center=geo.params["x0"])
geo.curved = dict(moleculeb=molec.snap)
phys = nano.Physics("pore_mol", geo, **physp)
solvers.set_sideBCs(phys, geop, physp)
R, H = float(geo.params["R"]), float(geo.params["H"])
print R, H
mesh2D = nano.RectangleMesh([-R, -H / 2.], [R, H / 2.], int(8 * R), int(4 * H))
#simplepnps.SimpleStokesProblem.method["kparams"].update(
# monitor_convergence = False,