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()