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
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 24 11:42:54 2016
@author: gregor
"""
import os
import dolfin
import nanopores.geometries.pughpore as pugh
import nanopores
nanopores.add_params(
z=0.,
r=1.,
)
print os.getpid()
geo = pugh.get_geo_cyl(x0=[1., 1., z], rMolecule=r) #rMolecule=0.15)
dolfin.plot(geo.subdomains)
dolfin.plot(geo.boundaries)
dolfin.interactive()