def geo_from_xml_threadsafe(name, reuse_mesh=False, clscale=None, **params):
import os, mpi4py
comm = mpi_comm_self()
if mpi4py.MPI.COMM_WORLD.Get_size() > 1:
pid = str(mpi4py.MPI.COMM_WORLD.Get_rank())
else:
pid = str(os.getpid())
if not reuse_mesh:
nanopores.generate_mesh(clscale, name, pid=pid, **params)
DIR = "%s/%s/mesh/" % (nanopores.DATADIR, name)
mesh = Mesh(comm, DIR + "mesh%s.xml" % pid)
subdomains = MeshFunction("size_t", mesh,
DIR + "mesh%s_physical_region.xml" % pid)
boundaries = MeshFunction("size_t", mesh,
DIR + "mesh%s_facet_region.xml" % pid)
with open(DIR + "meta%s.txt" % pid, "r") as f:
meta = eval(f.read())
physdom = meta.pop("physical_domain")
physbou = meta.pop("physical_boundary")
module = "nanopores.geometries.%s.params_geo" % name
params = nanopores.import_vars(module)
params.update(meta)
params["name"] = name
syn = params.pop("synonymes")
return Geometry(None, mesh, subdomains, boundaries, physdom, physbou, syn,
params)
def geo_from_xml(name):
DIR = "%s/%s/mesh/" %(nanopores.DATADIR, name)
mesh = Mesh(DIR+"mesh.xml")
subdomains = MeshFunction("size_t", mesh, filename=DIR+"mesh_physical_region.xml")
boundaries = MeshFunction("size_t", mesh, filename=DIR+"mesh_facet_region.xml")
with open(DIR+"meta.txt", "r") as f:
meta = eval(f.read())
physdom = meta.pop("physical_domain")
physbou = meta.pop("physical_boundary")
module = "nanopores.geometries.%s.params_geo" %name
params = nanopores.import_vars(module)
params.update(meta)
params["name"] = name
syn = params.pop("synonymes")
return Geometry(None, mesh, subdomains, boundaries, physdom, physbou, syn, params)
from nanopores import generate_mesh, geo_from_name, Poisson, PoissonProblem, qq, PB, PBProblem, import_vars, params_physical, get_mesh, u_to_matlab, IllposedNonlinearSolver
from dolfin import *
from random import random
t = Timer("time")
geo_name = "Nanowire"
globals().update(import_vars("nanopores.%s.params_geo" % geo_name))
def random_dopant_positions(N, **params):
# create N random points in unit cube
x = [[random() for i in range(3)] for i in range(N)]
# affine transformation on transducer
rr = params["r_eff"]
ll = params["l"]
T = lambda x : [x[0]*(w_core - 2*rr) + x_core + rr, x[1]*(ll - 2*rr) + rr,
x[2]*(h_core - 2*rr) + z_core + rr]
return map(T, x)
N = 5 # number of impurity atoms in pore
l = 10 # length of wire [nm]
clscale = 1.0 # mesh width scale
Nsamples = 1 # number of samples
r_eff = 3 # effective radius [nm]
voltage = -3 # voltage drop across 1000 nm wire [V]
# change physical parameters
#params_physical.permanent_charge["impurity"] = 1e6
#params_physical.permittivity["impurity"] = ???
#params_physical.ion_concentration["impurity"] = ???
geo_params = dict(l = l*1e-9, r_eff = r_eff*1e-9, lc = 10e-9)
# (c) 2017 Gregor Mitscha-Baude
from nanopores import geo_from_name, generate_mesh, user_params, import_vars
geo_name = "W_2D_geo"
geo_dict = import_vars("nanopores.geometries.%s.params_geo" % geo_name)
physical_dict = import_vars("nanopores.physics.params_physical")
default_dict = dict(geo_dict=geo_dict, physical_dict=physical_dict)
nm = geo_dict["nm"]
lsam = geo_dict["lsam"]
params = dict(
x0=[0, 0, 0],
outerfrac=0.2,
lsam=lsam,
r0=13 * nm - lsam,
angle=40,
sam=None,
)
generate_mesh(1., geo_name, **params)
geo = geo_from_name(geo_name, **params)
geo.plot_boundaries()
geo.plot_subdomains(interactive=True)