import matplotlib
import nanopores as nano
import nanopores.geometries.pughpore as pughpore
import matplotlib.pyplot as plt
from matplotlib.ticker import FormatStrFormatter
import numpy as np
import os
import sys
import nanopores.tools.fields as f
curr = 752.3849
HOME = os.path.expanduser("~")
PAPERDIR = os.path.join(HOME, "papers", "paper-howorka")
FIGDIR = os.path.join(PAPERDIR, "figures", "")
DATADIR = os.path.join(HOME, "Dropbox", "nanopores", "fields")
f.set_dir(DATADIR)
number = False
geop = nano.Params(pughpore.params)
hpore = geop.hpore
#fieldsname='eventsnew_both_1_'
#params=dict(avgbind1=23e6,avgbind2=3e4,P_bind1=0.035,P_bind2=3e-1,z0=hpore/2.+0.)
#i=350
def save_fig_filter(params, fieldsname, i):
data = f.get_fields(fieldsname, **params)
T_ = data["T"][i].load()
J_ = data["J"][i].load()
# (c) 2016 Gregor Mitscha-Baude
from dolfin import *
from nanopores.tools import fields
# set save/load directory
fields.set_dir("/tmp/nanopores/")
mesh = UnitSquareMesh(10, 10)
V = FunctionSpace(mesh, "CG", 1)
u = Function(V)
u.interpolate(Expression("sin(x[0]*x[1]*4*pi)"))
if not fields.exists("test_save"):
fields.save_functions("test_save", {}, utest=u)
fields.update()
functions, mesh = fields.get_functions("test_save")
u1 = functions["utest"]
plot(u1, interactive=True)
from matplotlib import pyplot as plt
import numpy as np
import os
from nanopores.tools import fields
from scipy.interpolate import interp1d
HOME = os.path.expanduser("~")
DATADIR = os.path.join(HOME, "Dropbox", "nanopores", "fields")
fields.set_dir(DATADIR)
data = fields.get_fields("pugh_diff3D_cross", bulkbc=True, rMolecule=2.0779)
def smooth3(l):
A = np.array(l)
B = A[:]
ker = np.array([1. / 3, 1. / 3, 1. / 3])
n = int(ker.shape[0] / 2.)
for i in range(n, A.shape[0] - n):
B[i] = np.inner(A[i - n:i + n + 1], ker)
return list(B)
def smooth5(l):
A = np.array(l)
B = A[:]
ker = np.array([.2, .2, .2, .2, .2])
n = int(ker.shape[0] / 2.)
for i in range(n, A.shape[0] - n):
B[i] = np.inner(A[i - n:i + n + 1], ker)
# (c) 2017 Gregor Mitscha-Baude
import numpy as np
import dolfin, os
import nanopores
from nanopores.models.pughpore import Plotter
from nanopores.models.diffusion_interpolation import get_pugh_diffusivity_alt
from nanopores.tools import fields
fields.set_dir(os.path.expanduser("~") + "/Dropbox/nanopores/fields")
params = nanopores.user_params(dim=3, r=2.0779, h=1., Nmax=.5e6)
functions = get_pugh_diffusivity_alt(**params)
D = functions["D"]
print D([0.,0.,0.])
#D = dolfin.as_matrix(np.diag([D[i] for i in range(params.dim)]))
plotter = Plotter()
plotter.plot(functions["D"][0], title="Dx")
plotter.plot(functions["D"][1], title="Dz")
plotter.plot(functions["dist"], title="dist")
dolfin.interactive()
